Method for evaluating oligonucleotide probe sequences

ABSTRACT

Methods are disclosed for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. A predetermined number of unique oligonucleotides is identified. The unique oligonucleotides are chosen to sample the entire length of a nucleotide sequence that is hybridizable with the target nucleotide sequence. At least one parameter that is independently predictive of the ability of each of the oligonucleotides of the set to hybridize to the target nucleotide sequence is determined and evaluated for each of the above oligonucleotides. A subset of oligonucleotides within the predetermined number of unique oligonucleotides is identified based on the evaluation of the parameter. Oligonucleotides in the subset are identified that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence. The method may be carried out with the aid of a computer.

This patent application includes a computer program listing appendix, which contains the source code for the software used in carrying out the examples in accordance with the present invention. The Appendix is contained on one compact disc submitted in duplicate designated as Copy 1 and Copy 2. The Appendix is in a single file that is 292 kB in size and named “computer program listing appendix U.S. Ser. No. 09-021,701”. The file was created on Feb. 2, 1998 and is a Microsoft Word document. The material in the Appendix is incorporated herein by reference.

A portion of the present disclosure contains material that is subject to copyright protection. The copyright owner has no objection to the facsimile reproduction by anyone of the patent document or the patent disclosure as it appears in the U.S. Patent and Trademark Office patent files or records, but otherwise reserves all copyright rights whatsoever.

BACKGROUND OF THE INVENTION

1. Field of the Invention

Significant morbidity and mortality are associated with infectious diseases and genetically inherited disorders. More rapid and accurate diagnostic methods are required for better monitoring and treatment of these conditions. Molecular methods using DNA probes, nucleic acid hybridization and in vitro amplification techniques are promising methods offering advantages to conventional methods used for patient diagnoses.

Nucleic acid hybridization has been employed for investigating the identity and establishing the presence of nucleic acids. Hybridization is based on complementary base pairing. When complementary single stranded nucleic acids, are incubated together, the complementary base sequences pair to form double-stranded hybrid molecules. The ability of single stranded deoxyribonucleic acid (ssDNA) or ribonucleic acid (RNA) to form a hydrogen bonded structure with a complementary nucleic acid sequence has been employed as an analytical tool in molecular biology research. The availability of radioactive nucleoside triphosphates of high specific activity and the development of methods for their incorporation into DNA and RNA has made it possible to identify, isolate, and characterize various nucleic acid sequences of biological interest. Nucleic acid hybridization has great potential in diagnosing disease states associated with unique nucleic acid sequences. These unique nucleic acid sequences may result from genetic or environmental change in DNA by insertions, deletions, point mutations, or by acquiring foreign DNA or RNA by means of infection by bacteria, molds, fungi, and viruses. The application of nucleic acid hybridization as a diagnostic tool in clinical medicine is limited due to the cost and effort associated with the development of sufficiently sensitive and specific methods for detecting potentially low concentrations of disease-related DNA or RNA present in the complex mixture of nucleic acid sequences found in patient samples.

One method for detecting specific nucleic acid sequences generally involves immobilization of the target nucleic acid on a solid support such as nitrocellulose paper, cellulose paper, diazotized paper, or a nylon membrane. After the target nucleic acid is fixed on the support, the support is contacted with a suitably labeled probe nucleic acid for about two to forty-eight hours. After the above time period, the solid support is washed several times at a controlled temperature to remove unhybridized probe. The support is then dried and the hybridized material is detected by autoradiography or by spectrometric methods. When very low concentrations must be detected, the above method is slow and labor intensive, and nonisotopic labels that are less readily detected than radio labels are frequently not suitable.

A method for the enzymatic amplification of specific segments of DNA known as the polymerase chain reaction (PCR) method has been described. This in vitro amplification procedure is based on repeated cycles of denaturation, oligonucleotide primer annealing, and primer extension by thermophilic polymerase, resulting in the exponential increase in copies of the region flanked by the primers. The PCR primers, which anneal to opposite strands of the DNA, are positioned so that the polymerase catalyzed extension product of one primer can serve as a template strand for the other, leading to the accumulation of a discrete fragment whose length is defined by the distance between the 5′ ends of the oligonucleotide primers.

Other methods for amplifying nucleic acids have also been developed. These methods include single primer amplification, ligase chain reaction (LCR), transcription-mediated amplification methods including 3SR and NASBA, and the Q-beta-replicase method. Regardless of the amplification used, the amplified product must be detected.

One method for detecting nucleic acids is to employ nucleic acid probes that have sequences complementary to sequences in the target nucleic acid. A nucleic acid probe may be, or may be capable of being, labeled with a reporter group or may be, or may be capable of becoming, bound to a support. Detection of signal depends upon the nature of the label or reporter group. Usually, the probe is comprised of natural nucleotides such as ribonucleotides and deoxyribonucleotides and their derivatives although unnatural nucleotide mimetics such as peptide nucleic acids and oligomeric nucleoside phosphonates are also used. Commonly, binding of the probes to the target is detected by means of a label incorporated into the probe. Alternatively, the probe may be unlabeled and the target nucleic acid labeled. Binding can be detected by separating the bound probe or target from the free probe or target and detecting the label. In one approach, a sandwich is formed comprised of one probe, which may be labeled, the target and a probe that is or can become bound to a surface. Alternatively, binding can be detected by a change in the signal-producing properties of the label upon binding, such as a change in the emission efficiency of a fluorescent or chemiluminescent label. This permits detection to be carried out without a separation step. Finally, binding can be detected by labeling the target, allowing the target to hybridize to a surface-bound probe, washing away the unbound target and detecting the labeled target that remains.

Direct detection of labeled target hybridized to surface-bound probes is particularly advantageous if the surface contains a mosaic of different probes that are individually localized to discrete, known areas of the surface. Such ordered arrays containing a large number of oligonucleotide probes have been developed as tools for high throughput analyses of genotype and gene expression. Oligonucleotides synthesized on a solid support recognize uniquely complementary nucleic acids by hybridization, and arrays can be designed to define specific target sequences, analyze gene expression patterns or identify specific allelic variations. One difficulty in the design of oligonucleotide arrays is that oligonucleotides targeted to different regions of the same gene can show large differences in hybridization efficiency, presumably due, at least in part, to the interplay between the secondary structures of the oligonucleotides and their targets and the stability of the final probe/target hybridization product. A method for predicting which oligonucleotides will show detectable hybridization would substantially decrease the number of iterations required for optimal array design and would be particularly useful when the total number of oligonucleotide probes on the array is limited. A method to predict oligonucleotide hybridization efficiency would also streamline the empirical approaches currently used to select potential antisense therapeutics, which are designed to modulate gene expression in vivo by hybridizing to specific messenger RNA (mRNA) molecules and inhibiting their translation into proteins.

While it is well known that the structure of the target nucleic acid affects the affinity of oligonucleotide hybridization, current methods for predicting target structures from the primary sequence fail to predict target regions accessible for oligonucleotide binding. Consequently, selection of oligonucleotides for antisense reagents or oligonucleotide probe arrays has been largely empirical. As most of the target sequence is sequestered by intramolecular base pairing and not accessible for oligonucleotide binding, the process of identifying good oligonucleotides has required large numbers of low efficiency experiments.

The design and implementation of algorithms that effectively predict the ability of oligonucleotides to rapidly and avidly bind to complementary nucleotide sequences has been an important problem in molecular biology since the invention of facile methods for chemical DNA synthesis. The subsequent inventions of the polymerase chain reaction (PCR), antisense inhibition of gene expression and oligonucleotide array methods for performing massively parallel hybridization experiments have made the need for effective predictive algorithms even more critical.

Previous attempts to solve the nucleic acid probe design problem include PCR primer design software applications (e.g., OLIGO®), neural networks, PCR primer design applications that search for sequences that possess minimal ability to cross-hybridize with other targets present in a sample (e.g., HYBsimulator™), and approaches that attempt to predict the efficiency of antisense sequence suppression of mRNA translation from a combination of predicted nucleic acid duplex melting temperature and predicted target strand structure. The methods that predict effective oligonucleotide primers for performing PCR from DNA templates work well for that application where relatively stringent conditions are employed. This is because PCR experimental design greatly simplifies the prediction problem: hybridization is performed at high temperature, at relatively low ionic strength and in the presence of a large molar excess of oligonucleotide. Under these conditions, the oligonucleotide and target secondary structures are relatively unimportant.

Unfortunately, these conditions do not apply to oligonucleotide arrays, which are usually hybridized under relatively non-denaturing conditions, or to antisense suppression of gene expression, which takes place in vivo. Oligonucleotide arrays can contain hundreds of thousands of different sequences and conditions are chosen to allow the oligonucleotide with the lowest melting temperature to hybridize efficiently. These “lowest common denominator” conditions are usually relatively non-denaturing and secondary structure constraints become significant. Accordingly, the above applications require new predictive methods that are capable of estimating the effects of oligonucleotide and target structure on hybridization efficiency. For these reasons, current algorithms for designing PCR primer oligonucleotides fail badly when applied to the problems of oligonucleotide array or antisense oligonucleotide design.

To date, the most effective approach for identifying oligonucleotides with good hybridization efficiency has been an empirical one. Such an approach involves the synthesis of large numbers of oligonucleotide probes for a given target nucleotide sequence. Arrays are formed that include the above oligonucleotide probes. Hybridization experiments are carried out to determine which of the oligonucleotide probes exhibit good hybridization efficiencies. Examples of such an approach are found in D. Lockhart, et al., Nature Biotech., infra, L. Wodicka, et al., Nature Biotechnology, infra., and N. Milner et al. Nature Biotech, infra. One major drawback to this approach is the vast number of oligonucleotides that must be synthesized in order to achieve a satisfactory result. Typically, about 2%-5% of the test probes synthesized yield acceptable signal levels.

The use of neural networks for oligonucleotide design has also been investigated. Neural networks are easily taught with real data; they therefore afford a general approach to many problems. However, their performance is limited by the “senses” that they are given. An analogy works best here: the human brain is an astoundingly capable neural network, but a blind person cannot be taught to reliably distinguish colors by smell. In addition, a large amount of data is required to adequately teach a neural network to perform its job well. A comprehensive database for either oligonucleotide array design or antisense suppression of gene expression has not been made available. For these reasons, the performance reported to-date of neural network solutions against the probe design problem is mediocre.

Finally, approaches that have attempted to use target nucleic acid folding calculations to predict experimental results inferred to depend upon hybridization efficiency (e.g. antisense suppression of mRNA translation) have so far only demonstrated that the predictions of current nucleic acid folding calculations correlate poorly with observed behavior. The probable reason for this is that the structures predicted by such programs for long sequences are poor predictors of chemical reality; the results of experiments that attempt to confirm the predictions of such calculations support this assessment. Recent improvements to this approach which use predicted RNA structure topology as a predictor of relative RNA/RNA association kinetics have been more successful at forecasting the results of antisense experiments. However, these methods are not computationally efficient, and have so far only been shown to work for targets less than 100 bases long. Such methods are therefore not yet capable of predicting the behavior of full-length mRNA targets, which are typically between 1,000 and 2,000 bases in length.

2. Description of the Related Art

U.S. Pat. No. 5,512,438 (Ecker) discloses the inhibition of RNA expression by forming a pseudo-half knot RNA at the target's RNA secondary structure using antisense oligonucleotides.

Cook, et al., in U.S. Pat. No. 5,670,633 discuss sugar-modified oligonucleotides that detect and modulate gene expression.

Antisense oligonucleotide inhibition of the RAS gene is disclosed in U.S. Pat. No. 5,582,986 (Monia, et al.).

U.S. Pat. No. 5,593,834 (Lane, et al.) discusses a method of preparing DNA sequences with known ligand binding characteristics.

Mitsuhashi, et al., in U.S. Pat. No. 5,556,749 discusses a computerized method for designing optimal DNA probes and an oligonucleotide probe design station.

U.S. Pat. No. 5,081,584 (Omichinski, et al.) discloses a computer-assisted design of anti-peptides based on the amino acid sequence of a target peptide.

A PCR primer design application that searches for sequences that possess minimal ability to cross-hybridize with other targets present in a sample is available as HYBsimulatorm™, version 2.0, AGCT, Inc., 2102 Business Center Drive, Suite 170, Irvine, Calif. 92715 (714) 833-9983.

A PCR primer design software application is available as OLIGO®, version 5.0, National Biosciences, Inc., 3650 Annapolis Lane North, #140, Plymouth, Minn. 55447 (800) 747-4362.

D. J. Lockhart, et al., Nature Biotech. 14:1675-1684 (1996) describe a neural network approach to the selection of efficient surface-bound oligonucleotide probes.

M. Mitsuhashi, etal., Nature, 367:759-761 (1994) disclose a method for designing specific oligonucleotide probes and primers by modeling the potential cross-hybridization of candidate probes to non-target sequences known to be present in samples.

R. A. Stull, et al., Nuc. Acids Res., 20:3501-3508 (1992) describe a method of predicting the efficacy of antisense oligonucleotides, using predicted target secondary structure and predicted oligonucleotide/target binding free energy as input parameters.

N. Milner, et al., Nature Biotechnology, 15:537-541 (1997) compare observed patterns of probe hybridization to those expected from the predicted secondary structure of the nucleic acid target.

L. Wodicka, et al., Nature Biotechnology, 15:1359-1367 (1997) describe simple rules for avoiding inefficient and non-specific probes during design and synthesis of oligonucleotides arrays.

J. SantaLucia Jr., et al., Biochemistry, 35:3555 (1996) disclose parameters and methods for the calculation of thermodynamic properties of DNA/DNA homoduplexes.

N. Sugimoto, et al., Biochemistry, 34:11211 (1995) disclose parameters and methods for the calculation of thermodynamic properties of DNA/RNA heteroduplexes.

J. A. Jaeger, et al., Proc. Natl. Acad. Sci. USA, 86:7706 (1989) disclose methods for estimation of the free energy of the most stable intramolecular structure of a single-stranded polynucleotide, by means of a dynamic programming algorithm.

S. F. Altschul, et al., Nature Genetics, 6:119-129 (1994) disclose methods for calculating the complexity and information content of amino acid and nucleic acid sequences.

T. A. Weber and E. Helfand, J. Chem. Phys., 71, 4760 (1979) describe approaches for the modeling of polymer structures by molecular dynamics simulations.

V. Patzel and G. Sczakiel, Nature Biotech., 16, 64-68 (1998) disclose methods for estimating rate constants for association of antisense RNA molecules with mRNA targets by examination of predicted antisense RNA secondary structures.

Light-generated oligonucleotide arrays for rapid DNA sequence analysis is described by A. C. Pease, et al., Proc. Nat. Acad. Sci. USA (1994) 91:5022-5026.

Mitsuhashi discusses basic requirements for designing optimal oligonucleotide probe sequences in J. Clinical Laboratory Analysis (1996) 10:277-284.

Rychlik, et al., discloses a computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA in Nucleic Acids Research (1989) 17(21):8543-8551.

A strategy for designing specific antisense oligonucleotide sequences is described by Mitsuhashi in J. Gastroenterol. (1997) 32:282-287.

Mitsuhashi discusses basic requirements for designing optimal PCR primers in J. Clinical Laboratory Analysis (1996) 10:285-293.

Hyndman, et al., disclose software to determine optimal oligonucleotide sequences based on hybridization simulation data in BioTechniques (1996) 20(6):1090-1094.

Eberhardt discloses a shell program for the design of PCR primers using genetics computer group (GCG) software (7.1) on VAX/VMS™ systems in BioTechniques (1992) 13(6):914-917.

Chen, et al., disclose a computer program for calculating the melting temperature of degenerate oligonucleotides used in PCR or hybridization in BioTechniques (1997) 22(6):1158-1160.

Partial thermodynamic parameters for prediction stability and washing behavior of DNA duplexes immobilized on gel matrix is described by Kunitsyn, et al., in J. Biomolecular Structure & Dynamics, ISSN 0739-1102 (1996) 14(1):239-244.

SUMMARY OF THE INVENTION

One embodiment of the present invention is a method for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. A predetermined set of unique oligonucleotide sequences is identified. The unique. oligonucleotide sequences are chosen to sample the entire length of a nucleotide sequence that is hybridizable with the target nucleotide sequence. At least one parameter that is predictive of the ability of each of the oligonucleotides specified by the set of sequences to hybridize to the target nucleotide sequence is determined and evaluated for each of the above oligonucleotide sequences. A subset of oligonucleotide sequences within the predetermined set of unique oligonucleotide sequences is identified based on the examination of the parameter values. Finally, oligonucleotide sequences in the subset are identified that are clustered along one or more regions of the nucleotide sequence that is hybridizable to the target nucleotide sequence. The oligonucleotide probes corresponding to the identified sequences find use in polynucleotide assays particularly where the assays involve oligonucleotide arrays. For a discussion of oligonucleotide arrays, see, e.g., U.S. Pat. No. 5,700,637 (E. Southern) and U.S. Pat. No. 5,667,667 (E. Southern), the relevant disclosures of which are incorporated herein by reference.

Another embodiment of the present invention is a method for predicting the potential of an oligonucleotide to hybridize to a complementary target nucleotide sequence. A set of overlapping oligonucleotide sequences is identified based on a nucleotide sequence that is complementary to the target nucleotide sequence. At least two parameters that are independently predictive of the ability of each of the oligonucleotides specified by the oligonucleotide sequences to hybridize to the target nucleotide sequence are determined and evaluated for each of the oligonucleotide sequences. Independence is assured by requiring that the parameters be poorly correlated with respect to one another. A subset of oligonucleotide sequences within the set of oligonucleotide sequences is identified based on the examination of the parameter values. Finally, oligonucleotide sequences in the subset are identified that are clustered along one or more regions of the nucleotide sequence that is complementary to the target nucleotide sequence.

Another embodiment of the present invention is a method for predicting the potential of an oligonucleotide to hybridize to a complementary target nucleotide sequence. A set of overlapping oligonucleotide sequences is obtained based on a nucleotide sequence of length L, complementary to the target nucleotide sequence. The oligonucleotide sequences of the set of overlapping oligonucleotide sequences are of identical length N and spaced one nucleotide apart. The set comprises L−N+1 oligonucleotide sequences. Parameters are determined for each of the oligonucleotide sequences of the set of overlapping oligonucleotide sequences. One parameter is the predicted melting temperature of the duplex of each of the oligonucleotides specified by the oligonucleotide sequences and the target nucleotide sequence, corrected for salt concentration. The other parameter is the predicted free energy of the most stable intramolecular structure of each of the oligonucleotides specified by the oligonucleotide sequences at the temperature of hybridization of the oligonucleotide with the target nucleotide sequence. A subset of oligonucleotide sequences within the set of oligonucleotide sequences is selected based on an examination of the parameter values by establishing cut-off values for each of the parameters. Oligonucleotide sequences in the subset that are clustered along one or more regions of the complementary nucleotide sequence are ranked based on the sizes of the clusters of oligonucleotide sequences. Finally, a subset of the clustered oligonucleotide sequences is selected that statistically samples the clusters of oligonucleotide sequences. The selected sampled subset is used to specify the synthesis of oligonucleotides for experimental evaluation.

Another aspect of the present invention is a computer based method for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. A predetermined number of unique oligonucleotides within a nucleotide sequence that is hybridizable with the target nucleotide sequence is identified under computer control. The oligonucleotides are chosen to sample the entire length of the nucleotide sequence. A value is determined and evaluated under computer control for each of the oligonucleotides for at least one parameter that is independently predictive of the ability of each of the oligonucleotides to hybridize to the target nucleotide sequence. The parameter values are stored. A subset of oligonucleotides within the predetermined number of unique oligonucleotides is identified by examination of the stored parameter values under computer control. Then, oligonucleotides in the subset that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence are identified under computer control.

Another aspect of the present invention is a computer system for conducting a method for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. The system comprises (a) input means for introducing a target nucleotide sequence into the computer system, (b) means for determining a number of unique oligonucleotide sequences that are within a nucleotide sequence that is hybridizable with the target nucleotide sequence where the oligonucleotide sequences are chosen to sample the entire length of the nucleotide sequence, (c) memory means for storing the oligonucleotide sequences, (d) means for controlling the computer system to carry out for each of the oligonucleotide sequences a determination and evaluation of a value for at least one parameter that is independently predictive of the ability of each of the oligonucleotide sequences to hybridize to the target nucleotide sequence, (e) means for storing the parameter values, (f) means for controlling the computer to carry out an identification from the stored parameter values a subset of oligonucleotide sequences within the number of unique oligonucleotide sequences based on the examination of the parameter, (g) means for storing the subset of oligonucleotides, (h) means for controlling the computer to carry out an identification of oligonucleotide sequences in the subset that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence, (i) means for storing the oligonucleotide sequences in the subset, and (j) means for outputting data relating to the oligonucleotide sequences in the subset.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a general flow chart depicting the method of the present invention.

FIG. 2 is a flow chart depicting a preferred embodiment of a method in accordance with the present invention.

FIG. 3 is a contour plot of normalized hybridization intensity from multiple experiments, as a function of the free energy of the most stable probe intramolecular structure (ΔG_(MFOLD)) and the difference between the predicted RNA/DNA heteroduplex melting temperature (T_(m)) and the temperature of hybridization (T_(hyb)).

FIG. 4 shows the observed hybridization patterns for oligonucleotides selected using a method in accordance with the present invention and additional oligonucleotides to a portion of the rabbit β-globin gene (radiolabeled antisense RNA target).

FIG. 5 shows the observed hybridization patterns for oligonucleotides selected using a method in accordance with the present invention and additional oligonucleotides to the HIV PRT gene (fluorescein-labeled sense RNA target).

FIG. 6 shows the observed hybridization patterns for oligonucleotides selected using a method in accordance with the present invention and additional oligonucleotides to the G3PDH gene (fluorescein-labeled antisense RNA target).

FIG. 7 shows the observed hybridization patterns for oligonucleotides selected using a method in accordance with the present invention and additional oligonucleotides to the p53 gene (fluorescein-labeled antisense RNA target).

FIG. 8 shows the observed hybridization patterns for oligonucleotides selected using a method in accordance with the present invention and additional oligonucleotides to the HIV PRTs gene (using data from the GeneChip™ data).

DEFINITIONS

Before proceeding further with a description of the specific embodiments of the present invention, a number of terms will be defined.

Nucleic Acids:

Polynucleotide—a compound or composition that is a polymeric nucleotide or nucleic acid polymer. The polynucleotide may be a natural compound or a synthetic compound. In the context of an assay, the polynucleotide is often referred to as a polynucleotide analyte. The polynucleotide can have from about 20 to 5,000,000 or more nucleotides. The larger polynucleotides are generally found in the natural state. In an isolated state the polynucleotide can have about 30 to 50,000 or more nucleotides, usually about 100 to 20,000 nucleotides, more frequently 500 to 10,000 nucleotides. It is thus obvious that isolation of a polynucleotide from the natural state often results in fragmentation. The polynucleotides include nucleic acids, and fragments thereof, from any source in purified or unpurified form including DNA (dsDNA and ssDNA) and RNA, including tRNA, mRNA, rRNA, mitochondrial DNA and RNA, chloroplast DNA and RNA, DNA/RNA hybrids, or mixtures thereof, genes, chromosomes, plasmids, the genomes of biological material such as microorganisms, e.g., bacteria, yeasts, viruses, viroids, molds, fungi, plants, animals, humans, and the like. The polynucleotide can be only a minor fraction of a complex mixture such as a biological sample. Also included are genes, such as hemoglobin gene for sickle-cell anemia, cystic fibrosis gene, oncogenes, cDNA, and the like.

The polynucleotide can be obtained from various biological materials by procedures well known in the art. The polynucleotide, where appropriate, may be cleaved to obtain a fragment that contains a target nucleotide sequence, for example, by shearing or by treatment with a restriction endonuclease or other site specific chemical cleavage method.

For purposes of this invention, the polynucleotide, or a cleaved fragment obtained from the polynucleotide, will usually be at least partially denatured or single stranded or treated to render it denatured or single stranded. Such treatments are well known in the art and include, for instance, heat or alkali treatment, or enzymatic digestion of one strand. For example, dsDNA can be heated at 90-100° C. for a period of about 1 to 10 minutes to produce denatured material.

Target nucleotide sequence—a sequence of nucleotides to be identified, usually existing within a portion or all of a polynucleotide, usually a polynucleotide analyte. The identity of the target nucleotide sequence generally is known to an extent sufficient to allow preparation of various sequences hybridizable with the target nucleotide sequence and of oligonucleotides, such as probes and primers, and other molecules necessary for conducting methods in accordance with the present invention, an amplification of the target polynucleotide, and so forth.

The target sequence usually contains from about 30 to 5,000 or more nucleotides, preferably 50 to 1,000 nucleotides. The target nucleotide sequence is generally a fraction of a larger molecule or it may be substantially the entire molecule such as a polynucleotide as described above. The minimum number of nucleotides in the target nucleotide sequence is selected to assure that the presence of a target polynucleotide in a sample is a specific indicator of the presence of polynucleotide in a sample. The maximum number of nucleotides in the target nucleotide sequence is normally governed by several factors: the length of the polynucleotide from which it is derived, the tendency of such polynucleotide to be broken by shearing or other processes during isolation, the efficiency of any procedures required to prepare the sample for analysis (e.g. transcription of a DNA template into RNA) and the efficiency of detection and/or amplification of the target nucleotide sequence, where appropriate.

Oligonucleotide—a polynucleotide, usually single stranded, usually a synthetic polynucleotide but may be a naturally occurring polynucleotide. The oligonucleotide(s) are usually comprised of a sequence of at least 5 nucleotides, preferably, 10 to 100 nucleotides, more preferably, 20 to 50 nucleotides, and usually 10 to 30 nucleotides, more preferably, 20 to 30 nucleotides, and desirably about 25 nucleotides in length.

Various techniques can be employed for preparing an oligonucleotide. Such oligonucleotides can be obtained by biological synthesis or by chemical synthesis. For short sequences (up to about 100 nucleotides), chemical synthesis will frequently be more economical as compared to the biological synthesis. In addition to economy, chemical synthesis provides a convenient way of incorporating low molecular weight compounds and/or modified bases during specific synthesis steps. Furthermore, chemical synthesis is very flexible in the choice of length and region of the target polynucleotide binding sequence. The oligonucleotide can be synthesized by standard methods such as those used in commercial automated nucleic acid synthesizers. Chemical synthesis of DNA on a suitably modified glass or resin can result in DNA covalently attached to the surface. This may offer advantages in washing and sample handling. For longer sequences standard replication methods employed in molecular biology can be used such as the use of M13 for single stranded DNA as described by J. Messing (1983) Methods Enzymol, 101:20-78.

Other methods of oligonucleotide synthesis include phosphotriester and phosphodiester methods (Narang, et al. (1979) Meth. Enzymol 68:90) and synthesis on a support (Beaucage, et al. (1981) Tetrahedron Letters 22:1859-1862) as well as phosphoramidite techniques (Caruthers, M. H., et al., “Methods in Enzymology,” Vol. 154, pp.287-314 (1988)) and others described in “Synthesis and Applications of DNA and RNA,” S. A. Narang, editor, Academic Press, New York, 1987, and the references contained therein. The chemical synthesis via a photolithographic method of spatially addressable arrays of oligonucleotides bound to glass surfaces is described by A. C. Pease, et al., Proc. Nat. Acad. Sci. USA (1994) 91:5022-5026.

Oligonucleotide probe—an oligonucleotide employed to bind to a portion of a polynucleotide such as another oligonucleotide or a target nucleotide sequence. The design and preparation of the oligonucleotide probes are generally dependent upon the sensitivity and specificity required, the sequence of the target polynucleotide and, in certain cases, the biological significance of certain portions of the target polynucleotide sequence.

Oligonucleotide primer(s)—an oligonucleotide that is usually employed in a chain extension on a polynucleotide template such as in, for example, an amplification of a nucleic acid. The oligonucleotide primer is usually a synthetic nucleotide that is single stranded, containing a sequence at its 3′-end that is capable of hybridizing with a defined sequence of the target polynucleotide. Normally, an oligonucleotide primer has at least 80%, preferably 90%, more preferably 95%, most preferably 100%, complementarity to a defined sequence or primer binding site. The number of nucleotides in the hybridizable sequence of an oligonucleotide primer should be such that stringency conditions used to hybridize the oligonucleotide primer will prevent excessive random non-specific hybridization. Usually, the number of nucleotides in the oligonucleotide primer will be at least as great as the defined sequence of the target polynucleotide, namely, at least ten nucleotides, preferably at least 15 nucleotides, and generally from about 10 to 200, preferably 20 to 50, nucleotides.

In general, in primer extension, amplification primers hybridize to, and are extended along (chain extended), at least the target nucleotide sequence within the target polynucleotide and, thus, the target sequence acts as a template. The extended primers are chain “extension products.” The target sequence usually lies between two defined sequences but need not. In general, the primers hybridize with the defined sequences or with at least a portion of such target polynucleotide, usually at least a ten-nucleotide segment at the 3′-end thereof and preferably at least 15, frequently a 20 to 50 nucleotide segment thereof.

Nucleoside triphosphates—nucleosides having a 5′-triphosphate substituent. The nucleosides are pentose sugar derivatives of nitrogenous bases of either purine or pyrimidine derivation, covalently bonded to the 1′-carbon of the pentose sugar, which is usually a deoxyribose or a ribose. The purine bases include adenine (A), guanine (G), inosine (I), and derivatives and analogs thereof. The pyrimidine bases include cytosine (C), thymine (T), uracil (U), and derivatives and analogs thereof. Nucleoside triphosphates include deoxyribonucleoside triphosphates such as the four common deoxyribonucleoside triphosphates dATP, dCTP, dGTP and dTTP and ribonucleoside triphosphates such as the four common triphosphates rATP, rCTP, rGTP and rUTP.

The term “nucleoside triphosphates” also includes derivatives and analogs thereof, which are exemplified by those derivatives that are recognized and polymerized in a similar manner to the underivatized nucleoside triphosphates.

Nucleotide—a base-sugar-phosphate combination that is the monomeric unit of nucleic acid polymers, i.e., DNA and RNA. The term “nucleotide” as used herein includes modified nucleotides as defined below.

DNA—deoxyribonucleic acid.

RNA—ribonucleic acid.

Modified nucleotide—a unit in a nucleic acid polymer that contains a modified base, sugar or phosphate group. The modified nucleotide can be produced by a chemical modification of the nucleotide either as part of the nucleic acid polymer or prior to the incorporation of the modified nucleotide into the nucleic acid polymer. For example, the methods mentioned above for the synthesis of an oligonucleotide may be employed. In another approach a modified nucleotide can be produced by incorporating a modified nucleoside triphosphate into the polymer chain during an amplification reaction. Examples of modified nucleotides, by way of illustration and not limitation, include dideoxynucleotides, derivatives or analogs that are biotinylated, amine modified, alkylated, fluorophore-labeled, and the like and also include phosphorothioate, phosphite, ring atom modified derivatives, and so forth.

Nucleoside—is a base-sugar combination or a nucleotide lacking a phosphate moiety.

Nucleotide polymerase—a catalyst, usually an enzyme, for forming an extension of a polynucleotide along a DNA or RNA template where the extension is complementary thereto. The nucleotide polymerase is a template dependent polynucleotide polymerase and utilizes nucleoside triphosphates as building blocks for extending the 3′-end of a polynucleotide to provide a sequence complementary with the polynucleotide template. Usually, the catalysts are enzymes, such as DNA polymerases, for example, prokaryotic DNA polymerase (I, II, or III), T4 DNA polymerase, T7 DNA polymerase, Klenow fragment, reverse transcriptase, Vent DNA polymerase, Pfu DNA polymerase, Taq DNA polymerase, and the like, or RNA polymerases, such as T3 and T7 RNA polymerases. Polymerase enzymes may be derived from any source such as cells, bacteria such as E. coli, plants, animals, virus, thermophilic bacteria, and so forth.

Amplification of nucleic acids or polynucleotides—any method that results in the formation of one or more copies of a nucleic acid or polynucleotide molecule (exponential amplification) or in the formation of one or more copies of only the complement of a nucleic acid or polynucleotide molecule (linear amplification).

Hybridization (hybridizing) and binding—in the context of nucleotide sequences these terms are used interchangeably herein. The ability of two nucleotide sequences to hybridize with each other is based on the degree of complementarity of the two nucleotide sequences, which in turn is based on the fraction of matched complementary nucleotide pairs. The more nucleotides in a given sequence that are complementary to another sequence, the more stringent the conditions can be for hybridization and the more specific will be the binding of the two sequences. Increased stringency is achieved by elevating the temperature, increasing the ratio of co-solvents, lowering the salt concentration, and the like.

Hybridization efficiency—the productivity of a hybridization reaction, measured as either the absolute or relative yield of oligonucleotide probe/polynucleotide target duplex formed under a given set of conditions in a given amount of time.

Homologous or substantially identical polynucleotides—In general, two polynucleotide sequences that are identical or can each hybridize to the same polynucleotide sequence are homologous. The two sequences are homologous or substantially identical where the sequences each have at least 90%, preferably 100%, of the same or analogous base sequence where thymine (T) and uracil (U) are considered the same. Thus, the ribonucleotides A, U, C and G are taken as analogous to the deoxynucleotides dA, dT, dC, and dG, respectively. Homologous sequences can both be DNA or one can be DNA and the other RNA.

Complementary—Two sequences are complementary when the sequence of one can bind to the sequence of the other in an anti-parallel sense wherein the 3′-end of each sequence binds to the 5′-end of the other sequence and each A, T(U), G, and C of one sequence is then aligned with a T(U), A, C, and G, respectively, of the other sequence. RNA sequences can also include complementary G/U or U/G base pairs.

Member of a specific binding pair (“sbp member”)—one of two different molecules, having an area on the surface or in a cavity that specifically binds to and is thereby defined as complementary with a particular spatial and polar organization of the other molecule. The members of the specific binding pair are referred to as cognates or as ligand and receptor (antiligand). These may be members of an immunological pair such as antigen-antibody, or may be operator-repressor, nuclease-nucleotide, biotin-avidin, hormones-hormone receptors, nucleic acid duplexes, IgG-protein A, DNA-DNA, DNA-RNA, and the like.

Ligand—any compound for which a receptor naturally exists or can be prepared.

Receptor (“antiligand”)—any compound or composition capable of recognizing a particular spatial and polar organization of a molecule, e.g., epitopic or determinant site. Illustrative receptors include naturally occurring receptors, e.g., thyroxine binding globulin, antibodies, enzymes, Fab fragments, lectins, nucleic acids, repressors, protection enzymes, protein A, complement component C1q, DNA binding proteins or ligands and the like.

Oligonucleotide Properties:

Potential of an oligonucleotide to hybridize—the combination of duplex formation rate and duplex dissociation rate that determines the amount of duplex nucleic acid hybrid that will form under a given set of experimental conditions in a given amount of time.

Parameter—a factor that provides information about the hybridization of an oligonucleotide with a target nucleotide sequence. Generally, the factor is one that is predictive of the ability of an oligonucleotide to hybridize with a target nucleotide sequence. Such factors include composition factors, thermodynamic factors, chemosynthetic efficiencies, kinetic factors, and the like.

Parameter predictive of the ability to hybridize—a parameter calculated from a set of oligonucleotide sequences wherein the parameter positively correlates with observed hybridization efficiencies of those sequences. The parameter is, therefore, predictive of the ability of those sequences to hybridize. “Positive correlation” can be rigorously defined in statistical terms. The correlation coefficient ρ_(x,y) of two experimentally measured discreet quantities x and y (N values in each set) is defined as ${\rho_{x,y} = \frac{{Covariance}\quad \left( {x,y} \right)}{\sqrt{{Variance}\quad (x){Variance}\quad (y)}}},$

where the Covariance (x,y) is defined by ${{Covariance}\quad \left( {x,y} \right)} = {\frac{1}{N}{\sum\limits_{j = 1}^{N}{\left( {x_{j} - \mu_{x}} \right){\left( {y_{j} - \mu_{y}} \right).}}}}$

The quantities μ_(x) and μ_(y) are the averages of the quantities x and y, while the variances are simply the squares of the standard deviations (defined below). The correlation coefficient is a dimensionless (unitless) quantity between −1 and 1. A correlation coefficient of 1 or −1 indicates that x and y have a linear relationship with a positive or negative slope, respectively. A correlation coefficient of zero indicates no relationship; for example, two sets of random numbers will yield a correlation coefficient near zero. Intermediate correlation coefficients indicate intermediate degrees of relatedness between two sets of numbers. The correlation coefficient is a good statistical measure of the degree to which one set of numbers predicts a second set of numbers.

Composition factor—a numerical factor based solely on the composition or sequence of an oligonucleotide without involving additional parameters, such as experimentally measured nearest-neighbor thermodynamic parameters. For instance, the fraction (G+C), given by the formula ${f_{GC} = \frac{n_{G} + n_{C}}{n_{G} + n_{C} + n_{A} + n_{T\quad {or}\quad U}}},$

where n_(G), n_(C), n_(A) and n_(T or U) are the numbers of G, C, A and T (or U) bases in an oligonucleotide, is an example of a composition factor. Examples of composition factors, by way of illustration and not limitation, are mole fraction (G+C), percent (G+C), sequence complexity, sequence information content, frequency of occurrence of specific oligonucleotide sequences in a sequence database and so forth.

Thermodynamic factor—numerical factors that predict the behavior of an oligonucleotide in some process that has reached equilibrium. For instance, the free energy of duplex formation between an oligonucleotide and its complement is a thermodynamic factor. Thermodynamic factors for systems that can be subdivided into constituent parts are often estimated by summing contributions from the constituent parts. Such an approach is used to calculate the thermodynamic properties of oligonucleotides.

Examples of thermodynamic factors, by way of illustration and not limitation, are predicted duplex melting temperature, predicted enthalpy of duplex formation, predicted entropy of duplex formation, free energy of duplex formation, predicted melting temperature of the most stable intramolecular structure of the oligonucleotide or its complement, predicted enthalpy of the most stable intramolecular structure of the oligonucleotide or its complement, predicted entropy of the most stable intramolecular structure of the oligonucleotide or its complement, predicted free energy of the most stable intramolecular structure of the oligonucleotide or its complement, predicted melting temperature of the most stable hairpin structure of the oligonucleotide or its complement, predicted enthalpy of the most stable hairpin structure of the oligonucleotide or its complement, predicted entropy of the most stable hairpin structure of the oligonucleotide or its complement, predicted free energy of the most stable hairpin structure of the oligonucleotide or its complement, thermodynamic partition function for intramolecular structure of the oligonucleotide or its complement and the like.

Chemosynthetic efficiency—oligonucleotides and nucleotide sequences may both be made by sequential polymerization of the constituent nucleotides. However, the individual addition steps are not perfect; they instead proceed with some fractional efficiency that is less than unity. This may vary as a function of position in the sequence. Therefore, what is really produced is a family of molecules that consists of the desired molecule plus many truncated sequences. These “failure sequences” affect the observed efficiency of hybridization between an oligonucleotide and its complementary target. Examples of chemosynthetic efficiency factors, by way of illustration and not limitation, are coupling efficiencies, overall efficiencies of the synthesis of a target nucleotide sequence or an oligonucleotide probe, and so forth.

Kinetic factor—numerical factors that predict the rate at which an oligonucleotide hybridizes to its complementary sequence or the rate at which the hybridized sequence dissociates from its complement are called kinetic factors. Examples of kinetic factors are steric factors calculated via molecular modeling or measured experimentally, rate constants calculated via molecular dynamics simulations, associative rate constants, dissociative rate constants, enthalpies of activation, entropies of activation, free energies of activation, and the like.

Predicted duplex melting temperature—the temperature at which an oligonucleotide mixed with a hybridizable nucleotide sequence is predicted to form a duplex structure (double-helix hybrid) with 50% of the hybridizable sequence. At higher temperatures, the amount of duplex is less than 50%; at lower temperatures, the amount of duplex is greater than 50%. The melting temperature T_(m) (° C.) is calculated from the enthalpy (ΔH), entropy (ΔS) and C, the concentration of the most abundant duplex component (for hybridization arrays, the soluble hybridization target), using the equation ${T_{m} = {\frac{\Delta \quad H}{{\Delta \quad S} + {R\quad \ln \quad C}} - 273.15}},$

where R is the gas constant, 1.987 cal/(mole-° K). For longer sequences (>100 nucleotides), T_(m) can also be estimated from the mole fraction (G+C), χ_(G+C), using the equation

 T_(m)=81.5+41.0_(χG+C).

Melting temperature corrected for salt concentration—polynucleotide duplex melting temperatures are calculated with the assumption that the concentration of sodium ion, Na⁺, is 1 M. Melting temperatures T′_(m) calculated for duplexes formed at different salt concentrations are corrected via the semi-empirical equation

T′_(m)([Na⁺])=T_(m)+16.6 log([Na⁺]).

Predicted enthalpy, entropy and free energy of duplex formation—the enthalpy (ΔH), entropy and free energy (ΔG) are thermodynamic state functions, related by the equation

ΔG=ΔH−T ΔS,

where T is the temperature in ° K. In practice, the enthalpy and entropy are predicted via a thermodynamic model of duplex formation (the “nearest neighbor” model which is explained in more detail below), and used to calculate the free energy and melting temperature.

Predicted free energy of the most stable intramolecular structure of an oligonucleotide or its complement—single-stranded DNA and RNA molecules that contain self-complementary sequences can form intramolecular secondary structures. For instance, the oligonucleotide

5′-ACTGGCAATCACAATTGCCAGTAA-3′ (SEQ ID NO:1)

can base pair with itself, to form the structure

where a vertical line indicates Watson-Crick base pair formation. Many such structures are possible for a given sequence; two are of particular interest. The first is the lowest energy “hairpin” structure (formed by folding a sequence back on itself with a connecting loop at least 3 nucleotides long). The second is the lowest energy structure that can be formed by including more complex topologies, such as “bulge loops” (unpaired duplexes between two regions of base-paired duplex) and cloverleaf structures, where 3 base-paired stretches meet at a triple-junction. A good example of a complex secondary structure is the structure of a tRNA molecule, an example of which, namely, yeast tRNA^(Ala) is shown below.

For either type of structure, a value of the free energy of that structure can be calculated, relative to the unpaired strand, by means of a thermodynamic model similar to that used to calculate the free energy of a base-paired duplex structure. Again, the free energy ΔG is calculated from the enthalpy ΔH and the entropy ΔS at a given absolute temperature T via the equation

ΔG=ΔH−T ΔS.

However, in this case there is the added difficulty that the lowest energy structure must be found. For a simple hairpin structure, this optimization can be performed via a relatively simple search algorithm. For more complex structures (such as a cloverleaf a dynamic programming algorithm, such as that implemented in the program MFOLD, must be used.

Yeast tRNA^(Ala)—The RNA sequence includes many non-standard ribonucleotides, such as D (5,6 dihydrouridine), m¹G (1-methylguanosine), m²G (N²-dimethylguanosine), ψ (pseudouridine), I (inosine), m¹I (1-methylinosine) and T (ribothymidine). Dots (•) mark (non-standard) G=U base pairs. The structure is taken from A. L. Lehninger, et al., Principles of Biochemistry, 2^(nd) Ed. (Worth Publishers, New York, N.Y., 1993).

Coupling efficiencies—chemosynthetic efficiencies are called coupling efficiencies when the synthetic scheme involves successive attachment of different monomers to a growing oligomer; a good example is oligonucleotide synthesis via phosphoramidite coupling chemistry.

Algorithmic Operations:

Evaluating a parameter—determination of the numerical value of a numerical descriptor of a property of an oligonucleotide sequence by means of a formula, algorithm or look-up table.

Filter—a mathematical rule or formula that divides a set of numbers into two subsets. Generally, one subset is retained for further analysis while the other is discarded. If the division into two subsets is achieved by testing the numbers against a simple inequality, then the filter is referred to as a “cut-off”. In the context of the current invention, an example by way of illustration and not limitation is the statement “The predicted self structure free energy must be greater than or equal to −0.4 kcal/mole,” which can be used as a filter for oligonucleotide sequences; this particular filter is also an example of a cut-off.

Filter set—A set of rules or formulae that successively winnow a set of numbers by identifying and discarding subsets that do not meet specific criteria. In the context of the current invention, an example by way of illustration and not limitation is the compound statement “the predicted self structure free energy must be greater than or equal to −0.4 kcal/mole and the predicted RNA/DNA heteroduplex melting temperature must lie between 600° C. and 85° C.,” which can be used as a filter set for oligonucleotide sequences.

Examining a parameter—comparing the numerical value of a parameter to some cutoff-value or filter.

Statistical sampling of a cluster—extraction of a subset of oligonucleotides from a cluster of oligonucleotides based upon some statistical measure, such as rank by oligonucleotide starting position in the sequence complementary to the target sequence.

First quartile, median and third quartile—If a set of numbers is ranked by value, then the value that divides the lower ¼ from the upper ¾ of the set is the first quartile, the value that divides the set in half is the median and the value that divides the lower ¾ from the upper ¼ of the set is the third quartile.

Poorly correlated—If it is not possible to perform a “good” prediction, as defined via statistics, of one set of numbers from another set of numbers using a simple linear model, then the two sets of numbers are said to be poorly correlated.

Computer program—a written set of instructions that symbolically instructs an appropriately configured computer to execute an algorithm that will yield desired outputs from some set of inputs. The instructions may be written in one or several standard programming languages, such as C, C++, Visual BASIC, FORTRAN or the like. Alternatively, the instructions may be written by imposing a template onto a general-purpose numerical analysis program, such as a spreadsheet.

Experimental System Components:

Small organic molecule—a compound of molecular weight less than 1500, preferably 100 to 1000, more preferably 300 to 600 such as biotin, fluorescein, rhodamine and other dyes, tetracycline and other protein binding molecules, and haptens, etc. The small organic molecule can provide a means for attachment of a nucleotide sequence to a label or to a support.

Support or surface—a porous or non-porous water insoluble material. The surface can have any one of a number of shapes, such as strip, plate, disk, rod, particle, including bead, and the like. The support can be hydrophilic or capable of being rendered hydrophilic and includes inorganic powders such as glass, silica, magnesium sulfate, and alumina; natural polymeric materials, particularly cellulosic materials and materials derived from cellulose, such as fiber containing papers, e.g., filter paper, chromatographic paper, etc.; synthetic or modified naturally occurring polymers, such as nitrocellulose, cellulose acetate, poly (vinyl chloride), polyacrylamide, cross linked dextran, agarose, polyacrylate, polyethylene, polypropylene, poly(4-methylbutene), polystyrene, polymethacrylate, poly(ethylene terephthalate), nylon, poly(vinyl butyrate), etc.; either used by themselves or in conjunction with other materials; glass available as Bioglass, ceramics, metals, and the like. Natural or synthetic assemblies such as liposomes, phospholipid vesicles, and cells can also be employed.

Binding of oligonucleotides to a support or surface may be accomplished by well-known techniques, commonly available in the literature. See, for example, A. C. Pease, et al, Proc. Nat. Acad. Sci. USA, 91:5022-5026 (1994).

Label—a member of a signal producing system. Usually the label is part of a target nucleotide sequence or an oligonucleotide probe, either being conjugated thereto or otherwise bound thereto or associated therewith. The label is capable of being detected directly or indirectly. Labels include (i) reporter molecules that can be detected directly by virtue of generating a signal, (ii) specific binding pair members that may be detected indirectly by subsequent binding to a cognate that contains a reporter molecule, (iii) oligonucleotide primers that can provide a template for amplification or ligation or (iv) a specific polynucleotide sequence or recognition sequence that can act as a ligand such as for a repressor protein, wherein in the latter two instances the oligonucleotide primer or repressor protein will have, or be capable of having, a reporter molecule. In general, any reporter molecule that is detectable can be used.

The reporter molecule can be isotopic or nonisotopic, usually non-isotopic, and can be a catalyst, such as an enzyme, a polynucleotide coding for a catalyst, promoter, dye, fluorescent molecule, chemiluminescent molecule, coenzyme, enzyme substrate, radioactive group, a small organic molecule, amplifiable polynucleotide sequence, a particle such as latex or carbon particle, metal sol, crystallite, liposome, cell, etc., which may or may not be further labeled with a dye, catalyst or other detectable group, and the like. The reporter molecule can be a fluorescent group such as fluorescein, a chemiluminescent group such as luminol, a terbium chelator such as N-(hydroxyethyl) ethylenediaminetriacetic acid that is capable of detection by delayed fluorescence, and the like.

The label is a member of a signal producing system and can generate a detectable signal either alone or together with other members of the signal producing system. As mentioned above, a reporter molecule can be bound directly to a nucleotide sequence or can become bound thereto by being bound to an sbp member complementary to an sbp member that is bound to a nucleotide sequence. Examples of particular labels or reporter molecules and their detection can be found in U.S. Pat. No. 5,508,178 issued Apr. 16, 1996, at column 11, line 66, to column 14, line 33, the relevant disclosure of which is incorporated herein by reference. When a reporter molecule is not conjugated to a nucleotide sequence, the reporter molecule may be bound to an sbp member complementary to an sbp member that is bound to or part of a nucleotide sequence.

Signal Producing System—the signal producing system may have one or more components, at least one component being the label. The signal producing system generates a signal that relates to the presence or amount of a target polynucleotide in a medium. The signal producing system includes all of the reagents required to produce a measurable signal. Other components of the signal producing system may be included in a developer solution and can include substrates, enhancers, activators, chemiluminescent compounds, cofactors, inhibitors, scavengers, metal ions, specific binding substances required for binding of signal generating substances, and the like. Other components of the signal producing system may be coenzymes, substances that react with enzymic products, other enzymes and catalysts, and the like. The signal producing system provides a signal detectable by external means, by use of electromagnetic radiation, desirably by visual examination. Signal-producing systems that may be employed in the present invention are those described more fully in U.S. Pat. No. 5,508,178, the relevant disclosure of which is incorporated herein by reference.

Ancillary Materials—Various ancillary materials will frequently be employed in the methods and assays utilizing oligonucleotide probes designed in accordance with the present invention. For example, buffers and salts will normally be present in an assay medium, as well as stabilizers for the assay medium and the assay components. Frequently, in addition to these additives, proteins may be included, such as albumins, organic solvents such as formamide, quaternary ammonium salts, polycations such as spermine, surfactants, particularly non-ionic surfactants, binding enhancers, e.g., polyalkylene glycols, or the like.

DETAILED DESCRIPTION OF THE INVENTION

The invention is directed to methods or algorithms for predicting oligonucleotides specific for a nucleic acid target where the oligonucleotides exhibit a high potential for hybridization. The algorithm uses parameters of the oligonucleotide and the oligonucleotide/target nucleotide sequence duplex, which can be readily predicted from the primary sequences of the target polynucleotide and candidate oligonucleotides. In the methods of the present invention, oligonucleotides are filtered based on one or more of these parameters, then further filtered based on the sizes of clusters of oligonucleotides along the input polynucleotide sequence. The methods or algorithms of the present invention may be carried out using either relatively simple user-written subroutines or publicly available stand-alone software applications (e.g., dynamic programming algorithm for calculating self-structure free energies of oligonucleotides). The parameter calculations may be orchestrated and the filtering algorithms may be implemented using any of a number of commercially available computer programs as a framework such as, e.g., Microsoft® Excel spreadsheet, Microsoft® Access relational database and the like. The basic steps involved in the present methods involve parsing a sequence that is complementary to a target nucleotide sequence into a set of overlapping oligonucleotide sequences, evaluating one or more parameters for each of the oligonucleotide sequences, said parameter or parameters being predictive of probe hybridization to the target nucleotide sequence, filtering the oligonucleotide sequences based on the values for each parameter, filtering the oligonucleotide sequences based on the length of contiguous sequence elements and ranking the contiguous sequence elements based on their length. We have found that oligonucleotides in the longest contiguous sequence elements generally show the highest hybridization efficiencies.

The present methods are based on our recognition that oligonucleotides showing high hybridization efficiencies tend to form clusters. It is believed that this clustering reflects local regions of the target nucleotide sequence that are unstructured and accessible for oligonucleotide binding. Oligonucleotides that are contiguous along a region of the input nucleic acid sequence are identified. These oligonucleotides are sorted based on the length of the contiguous sequence elements. The sorting approach used in the present invention apparently serves as a surrogate for the calculation of local secondary structure of the target a nucleotide sequence. This is supported by our observation that treatments intended to eliminate long-range nucleic acid structure (e.g., random fragmentation) do not eliminate the differences in hybridization yields across oligonucleotide probe arrays. This implies that major determinants of efficient hybridization are local regions of the target sequence. The identification of contiguous sequence elements is a simple and efficient method for recognizing clusters of such determinants and, thus, for identifying oligonucleotide probes that exhibit high hybridization efficiency for a target nucleotide sequence.

As mentioned above one embodiment of the present invention is a method for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. A predetermined number of unique oligonucleotides is identified. The length of the oligonucleotides may be the same or different. The oligonucleotides are unique in that no two of the oligonucleotides are identical. The unique oligonucleotides are chosen to sample the entire length of a nucleotide sequence that is hybridizable with the target nucleotide sequence. The actual number of oligonucleotides is generally determined by the length of the nucleotide sequence and the desired result. The number of oligonucleotides should be sufficient to achieve a consensus behavior. In other words, the oligonucleotide sequences should be sufficiently numerous that several possible probes overlap or fall within a given region that is expected to yield acceptable hybridization efficiency. Since the location of these regions is not known before hand, the best strategy is to equally space the probe sequences along the sequence that is hybridizable to the target sequence. Since regions of acceptable hybridization efficiency are generally on the order of 20 nucleotides in length, a practical strategy is to space the starting nucleotides of the oligonucleotide sequences no more than five base pairs apart. If computation time needed to calculate the predictive parameters is not an issue, then the best strategy is to space the starting nucleotides one nucleotide apart. An important feature of the present invention is to determine oligonucleotides that are clustered along a region of the nucleotide sequence. The individual predictions made for individual oligonucleotide sequences are not very good. However, we have found that the predictions that are experimentally observed tend to form contiguous clusters, while the spurious predictions tend to be solitary. Thus, the number of oligonucleotides should be sufficient to achieve the desired clustering.

Preferably, a set of overlapping sequences is chosen. To this end, the subsequences are chosen so that there is overlap of at least one nucleotide from one oligonucleotide to the next. More preferably, the overlap is two or more nucleotides. Most preferably, the oligonucleotides are spaced one nucleotide apart and the predetermined number is L−N+1 oligonucleotides where L is the length of the nucleotide sequence and N is the length of the oligonucleotides. In the latter situation, the unique oligonucleotides are of identical length N. Thus, a set of overlapping oligonucleotides is a set of oligonucleotides that are subsequences derived from some master sequence by subdividing that sequence in such a way that each subsequence contains either the start or end of at least one other subsequence in the set.

An example of the above for purposes of illustration and not limitation is presented by the sequence ATGGACTTAGCATTCG (SEQ ID NO:3), from which the following set of overlapping oligonucleotides can be identified:

ATGGACTTAGCA (SEQ ID NO:4)  TGGACTTAGCAT (SEQ ID NO:5)    GGACTTAGCATT (SEQ ID NO:6)    GACTTAGCATTC (SEQ ID NO:7)     ACTTAGCATTCG (SEQ ID NO:8)

In this example the overlapping oligonucleotides are spaced one nucleotide apart. In other words, there is overlap of all but one nucleotide from one oligonucleotide to the next. In the example above, the original nucleotide sequence is 16 nucleotides long (L=16). The length of each of the overlapping oligonucleotides is 12 nucleotides long (N=12) and there are L−N+1=5 oligonucleotides.

The length of the oligonucleotides may be the same or different and may vary depending on the length of the nucleotide sequence. The length of the oligonucleotides is determined by a practical compromise between the limits of current chemistries for oligonucleotide synthesis and the need for longer oligonucleotides, which exhibit greater binding affinity for the target sequence and are more likely to occur only once in complicated mixtures of polynucleotide targets. Usually, the length of the oligonucleotides is from about 10 to 50 nucleotides, more usually, from about 25 to 35 nucleotides.

In the next step of the method at least one parameter that is independently predictive of the ability of each of the oligonucleotides of the set to hybridize to the target nucleotide sequence is determined and evaluated for each of the above oligonucleotides. Examples of such a parameter, by way of illustration and not limitation, is a parameter selected from the group consisting of composition factors, thermodynamic factors, chemosynthetic efficiencies, kinetic factors and mathematical combinations of these quantities.

The determination of a parameter may be carried out by known methods. For example, melting temperature of the oligonucleotide/target duplex may be determined using the nearest neighbor method and parameters appropriate for the nucleotide acids involved. For DNA/DNA parameters, see J. SantaLucia Jr., et al., (1996) Biochemistry, 35:3555. For RNA/DNA parameters, see N. Sugimoto, et al., (1995) Biochemistry, 34:11211. Briefly, these methods are based on the observation that the thermodynamics of a nucleic acid duplex can be modeled as the sum of a term arising from the entire duplex and a set of terms arising from overlapping pairs of nucleotides (“nearest neighbor” model). For a discussion of the nearest neighbor see J. SantaLucia Jr., et al., (1996) Biochemistry, supra, and N. Sugimoto, et al., (1995) Biochemistry, supra. For example, the enthalpy ΔH of the duplex formed by the sequence

ATGGACTTAGCA (SEQ ID NO:4)

and its perfect complement can be approximated by the equation

ΔH {tilde over (=)}H_(init)+H_(AT)+H_(TG)+H_(GG)+H_(GA)+H_(AC)+H_(CT)+H_(TT)+H_(TA)+H_(AG)+H_(GC)+H_(CA).

In the above equation, the term Hinit is the initiation enthalpy for the entire duplex, while the terms H_(AT), . . . , H_(CA) are the so-called “nearest neighbor” enthalpies. Similar equations can be written for the entropy, for the corresponding quantities for RNA homoduplexes, or for DNA/RNA heteroduplexes. The free energy can then be calculated from the enthalpy, entropy and absolute temperature, as described previously.

Predicted free energy of the most stable intramolecular structure of an oligonucleotide (ΔG_(MFOLD)) may be determined using the nucleic acid folding algorithm MFOLD and parameters appropriate for the oligonucleotide, e.g., DNA or RNA. For MFOLD, see J. A. Jaeger, et al., (1989), supra. For DNA folding parameters, see J. SantaLucia Jr., et al., (1996), supra. Briefly, these methods operate in two steps. First, a map of all possible compatible intramolecular base pairs is made. Second, the global minimum of the free energy of the various possible base pairing configurations is found, using the nearest neighbor model to estimate the enthalpy and entropy, the user input temperature to complete the calculation of free energy, and a dynamic programming algorithm to find the global minimum. The algorithm is computationally intensive; calculation times scale as the third power of the sequence length.

The following Table 1 summarizes groups of parameters that are independently predictive of the ability of each of the oligonucleotides to hybridize to the target nucleotide sequence together with a reference to methods for their determination. Parameters within a given group are known or expected to be strongly correlated to one another, while parameters in different groups are known or expected to be poorly correlated with one another.

TABLE 1 Group Parameter Source or Reference I duplex enthalpy, ΔH Santa Lucia et al., 1996; Sugimoto et al., 1995 duplex entropy, ΔS Santa Lucia et al., 1996; Sugimoto et al., 1995 duplex free energy, ΔG ΔG = ΔH − TΔS (see text) melting temperature, T_(m) (see text) mole fraction (or percent) G + C self-explanatory subsequence duplex enthalpy Santa Lucia et al., 1996; Sugimoto et al., 1995 subsequence duplex entropy Santa Lucia et al., 1996; Sugimoto et al., 1995 subsequence duplex free energy ΔG = ΔH − TΔS (see text) subsequence duplex T_(m) (see text) subsequence duplex mole fraction self-explanatory (or percent) G + C II intramolecular enthalpy, ΔH_(MFOLD) Jaeger et al., 1989; Santa Lucia et al., 1996 intramolecular entropy, ΔS_(MFOLD) Jaeger et al., 1989; Santa Lucia et al., 1996 intramolecular free energy, ΔG_(MFOLD) ΔG = ΔH − TΔS (see text) hairpin enthalpy, ΔH_(hairpin) Jaeger et al., 1989; Santa Lucia et al., 1996 hairpin entropy, ΔS_(hairpin) Jaeger et al., 1989; Santa Lucia et al., 1996 hairpin free energy, ΔG_(hairpin) ΔG = ΔH − TΔS (see text) intramolecular partition function, Z $Z = {\sum\limits_{k\quad {structures}}\quad {\exp \left( {{- {\Delta G}_{intramolecular}^{(k)}}/{RT}} \right)}}$

III sequence complexity Altschul et al., 1994 sequence information content Altschul et al., 1994 IV steric factors molecular modeling or experiment molecular dynamic simulation Weber & Hefland, 1979 enthalpy, entropy & free energy of measured experimentally activation association & dissociation rates Patzel & Sczakiel, 1998 V oligonucleotide chemosynthetic measured experimentally efficiencies VI target synthetic efficiencies measured experimentally

In a next step of the present method, a subset of oligonucleotides within the predetermined number of unique oligonucleotides is identified based on the above evaluation of the parameter. A number of mathematical approaches may be followed to sort the oligonucleotides based on a parameter. In one approach a cut-off value is established. The cut-off value is adjustable and can be optimized relative to one or more training data sets. This is done by first establishing some metric for how well a cutoff value is performing; for example, one might use the normalized signal observed for each oligonucleotide in the training set. Once such a metric is established, the cutoff value can be numerically optimized to maximize the value of that metric, using optimization algorithms well known to the art. Alternatively, the cutoff value can be estimated using graphical methods, by graphing the value of the metric as a function of one or more parameters, and then establishing cutoff values that bracket the region of the graph where the chosen metric exceeds some chosen threshold value. In essence, the cut off values are chosen so that the rule set used yields training data that maximizes the inclusion of oligonucleotides that exhibit good hybridization efficiency and minimizes the inclusion of oligonucleotides that exhibit poor hybridization efficiency.

A preferred approach to performing such a graph-based optimization of filter parameters is shown in FIG. 3. In FIG. 3, hybridization data from several different genes have been used to prepare a contour plot of relative hybridization intensity as a function of DNA/RNA heteroduplex melting temperature and free energy of the most stable intramolecular structure of the probe. Contours are shown only for regions for which there are data; the white space outside of the outermost contour indicates that there are no experimental data for that region. The details of how the data were obtained can be found in Example 1 below. A summary of the sequences and number of data points employed is shown in Table 2 below. The measured hybridization intensities for each data set were normalized prior to construction of the contour plot depicted in FIG. 3 by dividing each observed intensity by the maximum intensity observed for that gene. In addition, differences in hybridization salt concentrations and hybridization temperatures were accounted for by using the salt concentration-corrected values of the melting temperatures and by subtracting the hybridization temperature from each predicted melting temperature, respectively. The filter set determined by examination of FIG. 3 is indicated by both the dotted open box in the figure and by the inequalities above the box.

One way in which such a contour plot may be prepared involves the use of an appropriate software application such as Microsoft® Excel® or the like. For example, the cross-abulation tool may be used in the Microsoft Excel® program. Data is accumulated into rectangular bins that are 0.5 kcal ΔG_(MFOLD) wide and 2.5° C. T_(m) wide. In each bin the average values of ΔG_(MFOLD), T_(m)−T_(hyb), and the normalized hybridization intensity are calculated. The data is output to the software application DeltaGraph® (Deltapoint, Inc., Monterey, Calif.) and the contour plot is prepared using the tools and instructions provided.

TABLE 2 Target (GenBank Target No. Data [Na⁺] Accession No.) Strand Points T_(hyb) Correction HIV protease-reverse Sense 1,022 35° C. −1.4° C. transcriptase (PRT)^(a) (M15654) HIV protease-reverse antisense 1,041 30° C. −1.4° C. transcriptase (PRT)^(a) (M15654) HIV protease-reverse Sense 88 35° C. −1.4° C. transcriptase (PRT)^(b) (M15654) Human G3PDH antisense 93 35° C. −1.4° C. (glyceraldehyde-3- dehydrogenase)^(b) (X01677) Human p53^(b) (X02469) antisense 93 35° C. −1.4° C. Rabbit β-globin^(c) (K03256) antisense 106 30° C.   0° C. ^(a)Data from Affymetrix GeneChip ™ Array ^(b)Data from biotinylated probes bound to streptavidin-coated microtiter wells ^(c)Literature data: see N. Milner, K. U. Mir & E. M. Southern (1997) Nature Biotech. 15, 537-541.

Once the cut-off value is selected, a subset of oligonucleotides having parameter values greater than or equal to the cut-off value is identified. This refers to the inclusion of oligonucleotides in a subset based on whether the value of a predictive parameter satisfies an inequality.

Examples of identifying a subset of oligonucleotides by establishing cut-off values for predictive parameters are as follows: for melting temperature an inequality might be 60° C.≦T_(m); for predicted free energy an inequality, preferably, might be ${\Delta \quad G_{MFOLD}} \geq {{- 0.4}\quad {\frac{kcal}{mole}.}}$

In a variation of the above, both a maximum and a minimum cut-off value may be selected. A subset of oligonucleotides is identified whose values fall within the maximum and minimum values, i.e., values greater than or equal to the minimum cut-off value and less than or equal to the maximum cut-off value. An example of this approach for melting temperature might be the inequality

60° C.≦T_(m)≦85° C.

With regard to cut off values for T_(m) the lower limit is most important, and is preferably T_(m)=T_(hyb), more preferably, T_(m)=T_(hyb)+15° C. The upper cutoff is important when the sequence region under consideration is unusually rich in G and C, and is preferably T_(m)=T_(hyb)+40° C. With regard to ΔG_(MFOLD) the cutoff value is usually greater than or equal to −1.0 kcal/mole. As mentioned above, the cutoff values preferably are determined from real data through experimental observations.

In another approach the parameter values may be converted into dimensionless numbers. The parameter value is converted into a dimensionless number by determining a dimensionless score for each parameter resulting in a distribution of scores having a mean value of zero and a standard deviation of one. The dimensionless score is a number that is used to rank some object (such as an oligonucleotide) to which that score relates. A score that has no units (i.e., a pure number) is called a dimensionless score.

In one approach the following equations are used for converting the values of said parameters into dimensionless numbers: ${s_{i,x} = \frac{x_{i} - {\langle x\rangle}}{\sigma_{\{ x\}}}},$

where S_(i,x) is the dimensionless score derived from parameter x calculated for oligonucleotide i, x_(i) is the value of parameter x calculated for oligonucleotide i, <x> is the average of parameter x calculated for all of the oligonucleotides under consideration for a given nucleotide sequence target, and σ_({x})is the standard deviation of parameter x calculated for all of the oligonucleotides under consideration for a given nucleotide sequence target, and is given by the equation ${\sigma_{\{ x\}} = \sqrt{\frac{\sum\limits_{j = 1}^{M}\left( {x_{j} - {\langle x\rangle}} \right)^{2}}{M - 1}}},$

where M is the number of oligonucleotides. The resulting distribution of scores, {S} has a mean value of zero and a standard deviation of one. These properties can be important for a combination of the scores discussed below.

The use of a dimensionless number approach may further include calculating a combination score S_(i) by evaluating a weighted average of the individual values of the dimensionless scores s_(i,x) by the equation: ${S_{i} = {\sum\limits_{\{ x\}}{q_{x}s_{i,x}}}},$

where q_(x) is the weight assigned to the score derived from parameter x, the individual values of q_(x) are always greater than zero, and the sum of the weights q_(x) is unity.

In another variation of the above approach, the method of calculation of the composite parameter is optimized based on the correlation of the individual composite scores to real data, as explained more fully below.

In one approach the calculation of the composite score further involves determining a moving window-averaged combination score <S_(i)> for the ith probe by the equation: ${{\langle S_{i}\rangle} = {\frac{1}{w}{\sum\limits_{j = {i - \frac{w - 1}{2}}}^{i + \frac{w - 1}{2}}S_{j}}}},\quad {w = {{an}\quad {odd}\quad {integer}}},$

where w is the length of the window for averaging (i.e., w nucleotides long), and then applying a cutoff filter to the value of <S_(i)>. This procedure results in smoothing (smoothing procedure) by turning each score into a consensus metric for a set of w adjacent oligonucleotide probes. The score, referred to as the “smoothed score,” is essentially continuous rather than a few discrete values. The value of the smoothed score is strongly influenced by clustering of scores with high or low values; window averaging therefore provides a measurement of cluster size.

An advantage of the dimensionless score approach to the probe prediction algorithm is that it is easy to objectively optimize. In one approach to training the algorithm, optimization of the weights q_(x) above may be performed by varying the values of the weights so that the correlation coefficient ρ_({<Si>},{Vi})between the set of window-averaged combination scores {<S_(i)>} and a set of calibration experimental measurements {V_(i)} is maximized. The correlation coefficient ρ_({<Si>},{Vi})is calculated from the equation ${\rho_{{\{{\langle S_{i}\rangle}\}},{\{ V_{i}\}}} = {\left( \frac{1}{M} \right)\frac{{Covariance}\quad \left( {{\langle S\rangle},V} \right)}{\sigma_{\{{\langle S_{i}\rangle}\}}\sigma_{\{ V_{i}\}}}}},$

where M is the number of window averaged, combination dimensionless scores and the number of corresponding measurements, the covariance is as defined earlier (see earlier equations) and σ_({<Si>})and σ_({Vi})are the standard deviations of {<S_(i)>} and {V_(i)}, as defined previously. An example of this approach is shown in Example 2, below.

In another approach the parameter is derived from one or more factors by mathematical transformation of the factors. This involves the calculation of a new predictive parameter from one or more existing predictive parameters, by means of an equation. For instance, the equilibrium constant K_(open) for formation of an oligonucleotide with no intramolecular structure from its structured form can be calculated from the intramolecular structure free energy ΔG_(MFOLD), using the equation $K_{open} = {\exp \quad {\left( \frac{\Delta \quad G_{MFOLD}}{R\quad T} \right).}}$

In a next step of the method oligonucleotides in the subset are then identified that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence. For example, consider a set of overlapping oligonucleotides identified by dividing a nucleotide sequence into subsequences. A subset of the oligonucleotides is obtained as described above. In general, this subset is obtained by applying a rule that rejects some members of the set. For the remaining members of the set, namely, the subset, there will be some average number of nucleotides in the nucleotide sequence between the first nucleotides of adjacent remaining subsequences. If, for some sub-region of the nucleotide sequence, the average number of nucleotides in the nucleotide sequence between the first nucleotides of adjacent remaining subsequences is less than the average for the entire nucleotide sequence, then the oligonucleotides are clustered. The smaller the average number of nucleotides between the first nucleotides of adjacent oligonucleotides, the stronger the clustering. The strongest clustering occurs when there are no intervening nucleotides between adjacent starting nucleotides. In this case, the oligonucleotides are said to be contiguous and may be referred to as contiguous sequence elements or “contigs.”

Accordingly, in this step oligonucleotides are sorted based on length of contiguous sequence elements. Oligonucleotides in the subset determined above are identified that are contiguous along a region of the input nucleic acid sequence. The length of each contigs that is equal to the number of oligonucleotides in each contigs, namely, oligonucleotides from the above step whose complement begin at positions m+1, m+2, . . . , m+k in the target sequence, form a contig of length k. Contigs can be identified and contig length can be calculated using, for example, a Visual Basic® module that can be incorporated into a Microsoft® Excel workbook.

Cluster size can be defined in several ways:

For contiguous clusters, the size is simply the number of adjacent oligonucleotides in the cluster. Again, this may also be referred to as contiguous sequence elements. The number may also be referred to as “contig length”. For example, consider the nucleotide sequence discussed above, namely, ATGGACTTAGCATTCG (SEQ ID NO:3) and the identified set of overlapping oligonucleotides

ATGGACTTAGCA (SEQ ID NO:4)  TGGACTTAGCAT (SEQ ID NO:5)   GGACTTAGCATT (SEQ ID NO:6)    GACTTAGCATTC (SEQ ID NO:7)     ACTTAGCATTCG (SEQ ID NO:8)

Suppose that, after calculation and evaluation of the predictive parameters, four nucleotides remain:

ATGGACTTAGCA     (SEQ ID NO:4)     TGGACTTAGCAT    (SEQ ID NO:5)     contig   GGACTTAGCATT   (SEQ ID NO:6)        ACTTAGCATTCG (SEQ ID NO:8)     single                                     oligonucleotide

A “contig” encompassing three of the oligonucleotides of the subset is present together with a single oligonucleotide. The contig length is 3 oligonucleotides.

Alternatively, cluster size at some position in the sequence hybridizable or complementary to the target sequence may be defined as the number of oligonucleotides whose center nucleotides fall inside a region of length M centered about the position in question, divided by M. This definition of clustering allows small gaps in clusters. In the example used above for contiguous clusters, if M was 10, then the cluster size would step through the values 0/10, . . . , 0/10, 1/10, 2/10, 3/10, 3/10, 4/10, 4/10, 4/10, 4/10, 4/10, 3/10, 2/10, 1/10, 1/10, 0/10 as the center of the window of length 10 passed through the cluster. In each fraction, the numerator is the number of oligonucleotide sequences that have satisfied the filter set and whose central nucleotides are within a window 10 nucleotides long, centered about the nucleotide under consideration. The denominator (10) is simply the window length.

Another alternative is to define the size of a cluster at some position in the sequence hybridizable or complementary to the target sequence as the number of oligonucleotide sequences overlapping that position. This definition is equivalent to the last definition with M set equal to the oligonucleotide probe length and omission of the division by M.

Finally, cluster size can be approximated at each position in a nucleotide sequence by dividing the sequence into oligonucleotides, evaluating a numerical score for each oligonucleotide, and then averaging the scores in the neighborhood of each position by means of a moving window average as described above. Window averaging has the effect of reinforcing clusters of high or low values around a particular position, while canceling varying values about that position. The window average, therefore, provides a score that is sensitive to both the hybridization potential of a given oligonucleotide and the hybridization potentials of its neighbors.

In a next step of the present method, the oligonucleotides in the subset are ranked. Generally, this ranking is based on the lengths of the clusters or contigs, sizes of the clusters or values of a window averaged score. Oligonucleotides found in the longest contigs or largest clusters, or possessing the highest window averaged scores usually show the highest hybridization efficiencies. Often, the highest signal intensity within the cluster corresponds to the median oligonucleotide of the cluster. However, the peak signal intensity within the contig can be determined experimentally, by sampling the cluster at its first quartile, midpoint and third quartile, measuring the hybridization efficiencies of the sampled oligonucleotides, interpolating or extrapolating the results, predicting the position of the optimal probe, and then iterating the probe design process.

FIG. 1 shows a diagram of an example of the above-described method by way of illustration and not limitation. Referring to FIG. 1 a target sequence of length L from, e.g., a database, is used to generate a sequence that is hybridizable to the target sequence from which candidate oligonucleotide probe sequences are generated. One or more parameters are calculated for each of the oligonucleotide probe sequences. The candidate oligonucleotide probe sequences are filtered based on the values of the parameters. Clustering of the filtered candidate probe sequences is evaluated and the clusters are ranked by size. Then, the oligonucleotide probes are statistically sampled and synthesized. Further evaluation may be made by evaluating the hybridization of the selected oligonucleotide probes in real hybridization experiments. The above process may be reiterated to further define the selection. In this way only a small fraction of the potential oligonucleotide probe candidates are synthesized and tested. This is in sharp contrast to the known method of synthesizing and testing all or a major portion of potential oligonucleotide probes for a given target sequence.

The methods of the present invention are preferably carried out at least in part with the aid of a computer. For example, an IBM® compatible personal computer (PC) may be utilized. The computer is driven by software specific to the methods described herein.

The preferred computer hardware capable of assisting in the operation of the methods in accordance with the present invention involves a system with at least the following specifications: Pentium® processor or better with a clock speed of at least 100 MHz, at least 32 megabytes of random access memory (RAM) and at least 80 megabytes of virtual memory, running under either the Windows 95 or Windows NT 4.0 operating system (or successor thereof).

As mentioned above, software that may be used to carry out the methods may be either Microsoft Excel or Microsoft Access, suitably extended via user written functions and templates, and linked when necessary to stand-alone programs that calculate specific parameters (e.g., MFOLD for intramolecular thermodynamic parameters). Examples of software programs used in assisting in conducting the present methods may be written, preferably, in Visual BASIC, FORTRAN and C++, as exemplified below in the Examples. It should be understood that the above computer information and the software used herein are by way of example and not limitation. The present methods may be adapted to other computers and software. Other languages that may be used include, for example, PASCAL, PERL or assembly language.

FIG. 2 depicts a more specific approach to a method in accordance with the present invention. Referring to FIG. 2, a sequence of length L is obtained from a database such as GenBank, UniGene or a proprietary sequence database. Probe length N is determined by the user based on the requirements for sensitivity and specificity and the limitations of the oligonucleotide synthetic scheme employed. The probe length and sequence length are used to generate L−N+1 candidate oligonucleotide probes, i.e., from every possible starting position. An initial selection is made based on local sequence predicted thermodynamic properties. To this end, melting temperature T_(m) and the self-structure free energy ΔG_(MFOLD), are calculated for each of the potential oligonucleotide probe: target nucleotide sequence complexes. Next, M probes that satisfy T_(m) and ΔG_(MFOLD) filters are selected. A further selection can be made based on clustering of “good” parameters. Good parameters are parameters that satisfy all of the filters in the filter set. Clustering is defined by any of the methods described previously; in FIG. 2, the “contig length” definition of clustering is used.

For each of the M oligonucleotide sequences that satisfied all filters the question is asked whether the oligonucleotide sequence immediately following the sequence under consideration is also one of the sequences that satisfied all of the filters. If the answer to this question is NO, then one stores the current value of the contig length counter, resets the counter to zero and proceeds to the next oligonucleotide sequence that satisfied all filters. If the answer to the question is YES, then 1 is added to the contig length counter and, if the counter now equals 1 (i.e., this is the first oligonucleotide probe sequence in the contig), the starting position of the oligonucleotide is stored. One then moves to the next oligonucleotide that satisfied all filters, which, in this case, is the same as the next oligonucleotide before the application of the filter set. The process is repeated until all M filtered oligonucleotide sequences have been examined. In this way, a single pass through the set of M filtered oligonucleotide sequences generates the lengths and starting positions of all contigs.

Next, contigs are ranked based on the lengths of their contiguous sequence elements. Longer contig lengths generally correlate with higher hybridization efficiencies. All oligonucleotides of the higher-ranking contigs may be considered, or candidate oligonucleotide probes may be picked. For example, candidate oligonucleotide probes can be picked one quarter, one half and three quarters of the way through each contig. The lafter approach provides local curvature determination after experimental determination of hybridization efficiencies, which allows either interpolation or extrapolation of the positions of the next probes to be synthesized in order to close in on the optimal probe in the region. If the contig brackets the actual peak of hybridization efficiency, the process will converge in 2-3 iterations. If the contig lies to one side of the actual peak, the process will converge in 3-4 iterations.

The above illustrative approach is further described with reference to the following DNA nucleotide sequence, which is the complement of the target RNA nucleotide sequence:

GTCCAAAAAGGGTCAGTCTACCTCCCGCCATAAAAAACTCATGTTCAAGA (SEQ ID NO:9).

In the first step of the method, the nucleotide sequence is divided into overlapping oligonucleotides that are 25 nucleotides in length. This length is chosen because it is an effective compromise between the need for sensitivity (enhanced by longer oligonucleotides) and the chemosynthetic efficiency of schemes for synthesis of surface-bound arrays of oligonucleotide probes.

Next, the estimated duplex melting temperatures (T_(m)) and self-structure free energies (ΔG_(MFOLD)) are calculated for each oligonucleotide in the set of overlapping oligonucleotides. The values are obtained from a user-written function that calculates DNA/RNA heteroduplex thermodynamic parameters (see N. Sugimoto, et al., Biochemistry, 34:11211 (1995)) and a modified version of the program MFOLD that estimates the free energy of the most stable intramolecular structure of a single stranded DNA molecule (see J. A. Jaeger, et al., (1989), supra, respectively. The steps are illustrated below.

GTCCAAAAAGGGTCAGTCTACCTCCCGCCATAAAAACTCATGTTCAAGA (target complement sequence) T_(m) (° C.) ΔG_(MFOLD) GTCCAAAAAGGGTCAGTCTACCTCC 71.77 −1.20 SEQ ID NO:10  TCCAAAAAGGGTCAGTCTACCTCCC 71.99 −1.20 SEQ ID NO:11   CCAAAAAGGGTCAGTCTACCTCCCG 70.78 −1.20 SEQ ID NO:12    CAAAAAGGGTCAGTCTACCTCCCGC 71.23 −1.20 SEQ ID NO:13      AAAAAGGGTCAGTCTACCTCCCGCC 73.07 −1.20 SEQ ID NO:14      AAAAGGGTCAGTCTACCTCCCGCCA 75.68 −1.20 SEQ ID NO:15        AAAGGGTCAGTCTACCTCCCGCCAT 77.53 −1.20 SEQ ID NO:16        AAGGGTCAGTCTACCTCCCGCCATA 79.03 −1.20 SEQ ID NO:17          AGGGTCAGTCTACCTCCCGCCATAA 79.03 −1.20 SEQ ID NO:18          GGGTCAGTCTACCTCCCGCCATAAA 76.85 −1.20 SEQ ID NO:19           GGTCAGTCTACCTCCCGCCATAAAA 73.10 −0.80 SEQ ID NO:20            GTCAGTCTACCTCCCGCCATAAAAA 69.50 0.90 SEQ ID NO:21             TCAGTCTACCTCCCGCCATAAAAAA 65.60 0.90 SEQ ID NO:22               CAGTCTACCTCCCGCCATAAAAAAC 64.96 0.90 SEQ ID NO:23               AGTCTACCTCCCGCCATAAAAAACT 65. 1.10 SEQ ID NO:24                 GTCTACCTCCCGCCATAAAAAACTC 66.36 2.40 SEQ ID NO:25                 TCTACCTCCCGCCATAAAAAACTCA 64.97 2.90 SEQ ID NO:26                   CTACCTCCCGCCATAAAAAACTCAT 63.96 2.70 SEQ ID NO:27                   TACCTCCCGCCATAAAAAACTCATG 62.58 1.10 SEQ ID NO:28                    ACCTCCCGCCATAAAAAACTCATGT 65.10 0.40 SEQ ID NO:29                      CCTCCCGCCATAAAAAACTCATGTT 64.96 0.10 SEQ ID NO:30                      CTCCCGCCATAAAAAACTCATGTTC 63.37 −0.10 SEQ ID NO:31                       TCCCGCCATAAAAAACTCATGTTCA 62.86 −0.10 SEQ ID NO:32                        CCCGCCATAAAAAACTCATGTTCAA 60.47 −0.10 SEQ ID NO:33                         CCGCCATAAAAAACTCATGTTCAAG 57.98 −0.10 SEQ ID NO:34                          CGCCATAAAAAACTCATGTTCAAGA 56.20 −0.10 SEQ ID NO:35

Next, the oligonucleotide sequences are filtered on the basis of T_(m). A high and low cut-off value may be selected, for example, 60° C.≦T_(m)≦85° C. Thus, oligonucleotides having T_(m) values falling within the above range are retained. Those outside the range are discarded, which is indicated below by lining out of those oligonucleotides and parameter values.

Next, the oligonucleotide sequences remaining after the above exercise are iltered on the basis of ΔG_(MFOLD) and are retained if the value is greater than −0.4. Those oligonucleotides with a ΔG_(MFOLD) less than −0.4 are discarded, which is indicated below by double lining out of those oligonucleotides and parameter values.

Clusters of retained oligonucleotides are identified and ranked based on cluster size. In this example, a contiguous cluster of 13 retained oligonucleotides is identified by the vertical black bar on the left. Any or all of the oligonucleotides in this cluster may be evaluated experimentally.

Alternatively, in one approach the oligonucleotides at the first quartile, the median and the third quartile of the cluster may be selected for experimental evaluation, indicated below by bold print.

In one aspect of the present method, at least two parameters are determined wherein the parameters are poorly correlated with respect to one another. The reason for requiring that the different parameters chosen are poorly correlated with one another is that an additional parameter that is strongly correlated to the original parameter brings no additional information to the prediction process. The correlation to the original parameter is a strong indication that both parameters represent the same physical property of the system. Another way of stating this is that correlated parameters are linearly dependent on one another, while poorly correlated parameters are linearly independent of one another. In practice, the absolute value of the correlation coefficient between any two parameters should be less than 0.5, more preferably, less than 0.25, and, most preferably, as close to zero as possible.

In one preferred approach instead of T_(m), for each oligonucleotide/target nucleotide sequence duplex, the difference between the predicted duplex melting temperature corrected for salt concentration and the temperature of hybridization of each of the oligonucleotides with the target nucleotide sequence is determined.

In one aspect the present method comprises determining two parameters at least one of the parameters being the association free energy between a subsequence within each of the oligonucleotides and its complementary sequence on the target nucleotide sequence, or some similar, strongly correlated parameter. The object of this approach is to identify a particularly stable subsequence of the oligonucleotide that might be capable of acting as a nucleation site for the beginning of the heteroduplex formation between the oligonucleotide and the target nucleotide sequence. Such nucleation is believed to be the rate-limiting step for process of heteroduplex formation.

The subsequence within the oligonucleotide is from about 3 to 9 nucleotides in length, usually, 5 to 7 nucleotides in length. The subsequence is at least three nucleotides from the terminus of the oligonucleotide. For support-bound oligonucleotides the subsequence is at least three nucleotides from the free end of the oligonucleotide, i.e., the end that is not attached to the support. Generally, this free end is the 5′ end of the oligonucleotide. When the oligonucleotide is attached to a support, the subsequence is at least three nucleotides from the end of the oligonucleotide that is bound to the surface of the support to which the oligonucleotide is attached. Generally, the 3′ end of the oligonucleotide is bound to the support.

The predictive parameter can be, for example, either melting temperature or duplex free energy of the subsequence with the target nucleotide sequence. The subsequence with the maximum (melting temperature) or minimum (free energy) value of one of the above parameters is chosen as the representative subsequence for that oligonucleotide probe. For example, if the oligonucleotide is nucleotides in length and a subsequence of 5 nucleotides is chosen, i.e., a 5-mer, then parameter values are calculated for all 5-mer subsequences of the oligonucleotide that do not include the 2 nucleotides at the free end of the oligonucleotide. Where 5′ is the free end of the oligonucleotide with designated nucleotide number 1, the values are calculated for all 5-mer subsequences with starting nucleotides from position number 3 to position number 16. Thus, in this example, parameter values for 14 different subsequences are calculated. The subsequence with the maximum value for the parameter is then assigned as the stability subsequence for the oligonucleotide.

The inclusion of the above determination of a stability subsequence results in the following algorithm for determining the potential of an oligonucleotide to hybridize to a target nucleotide sequence. A predetermined number of unique oligonucleotides are identified within a nucleotide sequence that is hybridizable with said target nucleotide sequence. The oligonucleotides are chosen to sample the entire length of the nucleotide sequence. For each of the oligonucleotides, parameters that are independently predictive of the ability of each of said oligonucleotides to hybridize to said target nucleotide sequence are determined and evaluated. Two parameters that may be used are the thermodynamic parameters of T_(m) and ΔG_(MFOLD). These parameters give rise to associated parameter filters. In one approach evaluation of the parameters involves establishing cut-off values as described above. Application of these cut-off values results in the identification of a subset of oligonucleotides for further scrutiny under the algorithm. In accordance with this embodiment of the present invention, there is included a stability subsequence limit in addition to the above. Cutoff values are determined either by means of objective optimization algorithms well known to the art or via graphical estimation methods; both approaches have been described previously in this document. In either case, the optimization of cutoff values involves comparison of predictions to known hybridization efficiency data sets. This process results in objective optimization as it looks at prediction versus experimental results and is otherwise referred to herein as “training the algorithm.” The experimental data used to train the algorithm is referred to herein as “training data.”

In the present approach filters are assigned to the T_(m) oligonucleotide probe data. The T_(m) of each oligonucleotide probe needs to be greater than or equal to the assigned filter (T_(m) probe limit) to be given a filter score of “1”; otherwise, the filter score is “0”. In addition, one can also impose a second filter for this parameter; that is, that the T_(m) of the oligonucleotide probe also has to be less than a defined upper limit. Filters are also assigned to the ΔG_(MFOLD) data. The ΔA_(GMFOLD) of each oligonucleotide probe should be greater than or equal to the assigned filter (ΔG_(MFOLD) limit) to be given a filter score of “1”; otherwise, the filter score is “0”. The filter scores are added. Furthermore, one can also impose a second filter for this parameter; that is, that the ΔG_(MFOLD) also has to be less than a defined upper limit. In accordance with the above discussion stability subsequences are identified. This leads to another filter. Accordingly, filters are assigned to the stability sequence data. The stability subsequence of each oligonucleotide probe needs to be greater than or equal to the assigned filter limit to be given a filter score of “1”; otherwise, the filter score is “0”. In addition, one can also impose a second filter for this parameter; that is, that the stability subsequence also has to be less than a defined upper limit. In all cases, the filter values are determined by objective optimization (algorithmic or graphical) of the predictions of the present method versus training data, as described previously.

On the basis of the above filter sets a subset of oligonucleotides within said predetermined number of unique oligonucleotides is identified. Oligonucleotides in the subset are identified that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence. The resulting number of oligonucleotide probe regions is examined. The above filters may then be loosened or tightened by changing the filter limits to obtain more or fewer clusters of oligonucleotides to match the goal, which is set by the needs of the investigator. For instance, a particular application might require that the investigator design 5 non-overlapping probes that efficiently hybridize to a given target sequence.

As mentioned above, the contigs may be selected on the basis of contig length. In another approach, the scores defined above may be summed for cluster size determination. To this end the probe score of the particular filter set (e.g., T_(m) probe limit, ΔG_(MFOLD) limit and stability sequence limit) is calculated for each oligonucleotide probe. The probe score is the sum of the filter scores. Thus, the probe score is 0 if no parameters pass their respective filters. The probe score is 1, 2 or 3 if one, two or three parameters, respectively, pass their filters for that oligonucleotide probe. This summing is continued for each parameter that is in the current filter set of the algorithm used. For a given algorithm a minimum probe score limit is set. In the current example this limit will be at least 1 and could be 2 or 3 depending on the needs of the investigator, the number of probe clusters required and the results of objective optimizations of algorithm performance against training data. The probe score is compared to this probe score limit. If the probe score of oligonucleotide probe i is greater than or equal to the probe score limit, then oligonucleotide probe i is assigned a score passed value of 1. Next, a window is chosen for the evaluation of clustering (the “cluster window”). This will be the next filter applied. The cluster window (“w”) smoothes the score passed values by summing the values in a window w nucleotides long, centered about position i. The resulting sum is called the cluster sum. Usually, the cluster window is an odd integer, usually 7 or 9 nucleotides. The cluster sum values are then filtered, by comparing to a user-set threshold, cluster filter. If cluster sum is greater than or equal to cluster filter, this filter is passed, and the probe is predicted to hybridize efficiently to its target.

This window summing procedure converts the score for the passed value for each oligonucleotide into a consensus metric for a set of w adjacent probes. A “consensus metric” is a measurement that distills a number of values into one consensus value. In this case, the consensus value is calculated by simply summing the individual values. The window summing procedure therefore evaluates a property similar to the contig length metric discussed above. However, the summed score has the advantage of allowing for a few probes within a cluster to have not passed their individual probe score limits. We have found that this allows more observed hybridization peaks to be predicted.

It may be desired in some circumstances to combine the results of multiple algorithm versions. We refer to this operation as “tiling”. This may be explained more fully as follows. Tiling generally involves joining together the predicted oligonucleotide probe sets identified by multiple algorithm versions. In the context of the present invention, tiling multiple algorithm versions involves forming the union of multiple sets of predictions. These predictions may arise from different embodiments of the present invention. Alternatively, the different sets of predictions may arise from the same embodiment, but different filter sets. The different filter sets may additionally be restricted to different combinations of parameter values. For instance, one filter set might be used when the predicted duplex melting temperature T_(m) is greater than or equal to some value, while another might be used when T_(m) is below that value.

An example of the logical endpoint of tiling multiple filter sets across different regions of the possible combinations of predictive parameters and then forming the union of the resulting predictions is the contour plot shown in FIG. 3, with the associated rule that “the value of the normalized hybridization intensity associated with a particular combination of (T_(m)−T_(hyb)) and ΔG_(MFOLD) must be greater than or equal to some threshold value.” In this case, the contour at the threshold value becomes the filter. This contour and its interior can be thought of as the union of many small rectangular regions (“tiles”), each of which is bracketed by low and high cutoff values for each of the parameters.

The predictions of different algorithm versions can also be combined by forming the intersection of two or more different predictions. The reliability of predictions within such intersection sets is enhanced because such sets are, by definition, insensitive to changes in the details of the predictive algorithm. Intersection is a useful method for reducing the number of predicted probes when a single algorithm version produces too many candidate probes for efficient experimental evaluation.

The most specific oligonucleotide probe set (i.e., the set least likely to include poor probes) will be the intersection set from multiple algorithms. Clusters that have overlapping oligonucleotide probes from multiple algorithms constitute the intersection set of oligonucleotide probes. The oligonucleotide probe that is in the center of an intersection cluster is chosen. This central oligonucleotide probe may have the highest probability of predicting a peak or, in other words, of binding well to the target nucleotide sequence. Oligonucleotide probes on either side of center, which are still within the intersection cluster, may also be selected. The distance of these “side” oligonucleotide probes from the center generally will be shorter or longer depending upon the length of the cluster.

The most sensitive set of oligonucleotide probes (i.e., the set most likely to include at least one good probe) is generally the union set from multiple algorithms. Clusters that are predicted by at least one type of algorithm constitute the union set of oligonucleotide probes. The oligonucleotide probe in the center of a union cluster is chosen. Oligonucleotide probes on either side of center, which are still within the union cluster, usually are also chosen. The distance of these side probes from the center will be shorter or longer depending upon the length of the cluster. In summary, the combination of using the stability subsequence parameter, tiling multiple filter sets, and making union and intersection cluster sets of oligonucleotide probes exhibits very high sensitivity and specificity in predicting oligonucleotide probes that effectively hybridize to a target nucleotide sequence of interest.

Another aspect of the present invention is a computer based method for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. A predetermined number of unique oligonucleotides within a nucleotide sequence that is hybridizable with the target nucleotide sequence is identified under computer control. The oligonucleotides are chosen to sample the entire length of the nucleotide sequence. A value is determined and evaluated under computer control for each of the oligonucleotides for at least one parameter that is independently predictive of the ability of each of the oligonucleotides to hybridize to the target nucleotide sequence. The parameter values are stored. Based on the examination of the stored parameter values, a subset of oligonucleotides within the predetermined number of unique oligonucleotides is identified under computer control. Then, oligonucleotides in the subset that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence are identified under computer control.

A computer program is utilized to carry out the above method steps. The computer program provides for input of a target-hybridizable or target-complementary nucleotide sequence, efficient algorithms for computation of oligonucleotide sequences and their associated predictive parameters, efficient, versatile mechanisms for filtering sets of oligonucleotide sequences based on parameter values, mechanisms for computation of the size of clusters of oligonucleotide sequences that pass multiple filters, and mechanisms for outputting the final predictions of the method of the present invention in a versatile, machine-readable or human-readable form.

Another aspect of the present invention is a computer system for conducting a method for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. An input means for introducing a target nucleotide sequence into the computer system is provided. The input means may permit manual input of the target nucleotide sequence. The input means may also be a database or a standard format file such as GenBank. Also included in the system is means for determining a number of unique oligonucleotide sequences that are within a nucleotide sequence that is hybridizable with the target nucleotide sequence. The oligonucleotide sequences is chosen to sample the entire length of the nucleotide sequence. Suitable means is a computer program or software, which also provides memory means for storing the oligonucleotide sequences. The system also includes means for controlling the computer system to carry out a determination and evaluation for each of the oligonucleotide sequences a value for at least one parameter that is independently predictive of the ability of each of the oligonucleotide sequences to hybridize to the target nucleotide sequence. Suitable means is a computer program or software such as, for example, Microsoft® Excel spreadsheet, Microsoft® Access relational database or the like, which also provides memory means for storing the parameter values. The system further comprises means for controlling the computer to carry out an identification of a subset of oligonucleotide sequences within the number of unique oligonucleotide sequences based on the automated examination of the stored parameter values. Suitable means is a computer program or software, which also allocates memory means for storing the subset of oligonucleotides. The system also includes means for controlling the computer to carry out an identification of oligonucleotide sequences in the subset that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence. Suitable means is a computer program or software, which also allocates memory means for storing the oligonucleotide sequences in the subset. The computer system also includes means for outputting data relating to the oligonucleotide sequences in the subset. Such means may be machine readable or human readable and may be software that communicates with a printer, electronic mail, another computer program, and the like. One particularly attractive feature of the present invention is that the outputting means may communicate directly with software that is part of an oligonucleotide synthesizer. In this way the results of the method of the present invention may be used directly to provide instruction for the synthesis of the desired oligonucleotides.

Another advantage of the present invention is that it may be used to predict efficient hybridization oligonucleotides for each of multiple target sequences. thus, very large arrays may be constructed and tested with minimal synthesis of ligonucleotides.

EXAMPLES

The invention is demonstrated further by the following illustrative examples. Parts and percentages are by weight unless otherwise indicated. Temperatures are in degrees Centigrade (° C.) unless otherwise specified. The following preparations and examples illustrate the invention but are not intended to limit its scope. All reagents used herein were from Amresco, Inc., Solon, Ohio (buffers), Pharmacia Biotech, Piscataway, N.J. (nucleoside triphosphates) or Promega, Madison, Wis. (RNA polymerases) unless indicated otherwise.

Example 1

Synopsis:

Data from labeled RNA target hybridizations to surface-bound DNA probes directed against 4 different gene sequences were compared to the predictions of the preferred version of the prediction algorithm illustrated by the flow chart in FIG. 2. The RNA targets were sequences derived from the human immunodeficiency virus protease-reverse transcriptase region (HIV PRT; sense-strand target polynucleotide), human glyceraldehyde-3-phosphate dehydrogenase gene (G3PDH; antisense-strand target polynucleotide), human tumor suppressor p53 gene (p53; antisense-strand target polynucleotide) and rabbit β-globin gene (β-globin; antisense-strand target polynucleotide). The GenBank accession numbers for the gene sequences, number of data points collected and temperature of hybridization have all been previously listed in Table 2.

Materials and Methods:

Three different experimental systems and two different labeling schemes were used to collect data.

The sequence and hybridization data for β-globin were taken from the literature (see Milner et al., (1997), supra; in this experiment, ³²P-radiolabeled RNA target was used.

The hybridization data for HIV PRT were obtained using an Affymetrix GeneChip™ HIV PRT-sense probe array (i.e. sense strand target polynucleotide) (GeneChip™ HIV PRT 440s, Affymetrix Corporation, Santa Clara, Calif.) as specified by the manufacturer, except that the fluorescein-labeled RNA target was not fragmented prior to hybridization and that hybridization was performed for 24 hours. The concentration of fluorescein-labeled RNA used was 26.3 nM; label density was approximately 18 fluoresceinated uridyl nucleotides per 1 kilobase (kb) RNA transcript. The raw data were collected by scanning the array with a GeneChip™ Scanner 50 (Affymetrix Corporation, Santa Clara, Calif.), as specified by the manufacturer. The raw data were reduced to a feature-averaged (“CEL”) file, using the GeneChip™ software supplied with the scanner. Finally, a table of hybridization intensities for perfect-complement 20-mer probes was constructed using the ASCII feature map file supplied with the GeneChip™ software to connect probe sequences to measured hybridization intensities. The resulting data set contained data for every overlapping 20-mer probe to the target sequence.

The data for G3PDH and p53 were measured using 93-feature arrays constructed using commercially available streptavidin-coated microtiter plates (Pierce Chemical Company, Rockford, Ill.). Every tenth possible 25-mer probe complementary to each target was synthesized and 3′-biotinylated by a contract synthesis vendor (Operon, Inc., Alameda, Calif.). The 3′-Iinked biotin was used to anchor individual probes to microtiter wells, via the well known, strong affinity of streptavidin for biotin. Biotinylated DNA probes were resuspended to a concentration of 10 μM in hybridization buffer (5×sodium chloride-sodium phosphate-disodium ethylenediaminetetraacetate (SSPE), 0.05% Triton X-100, filter-sterilized; 1×SSPE is 150 mM sodium chloride, 10 mM sodium phosphate, 1 mM disodium ethylenediaminetetraacetate (EDTA), pH 7.4). Individual probes were diluted 1:10 in hybridization buffer into specified wells (100 μl total volume per well) of a streptavidin-coated microtiter plate; probes were allowed to bind to the covered plates overnight at 35° C. The other 3 wells of the 96-well microtiter plate were probe-less controls. The coated plates were washed with 3×200 μl of wash buffer (6×SSPE, 0.005% Triton X-100, filter-sterilized). Fluorescein-labeled RNA (100 μl of a 10 nM solution in hybridization buffer) was added to each well. The plates were covered and hybridized at 35° C. for 20-24 hours. The hybridized plates were washed with 3×200 μl of wash buffer. Label was then released in each well by adding 100 μl of 20 μg/ml RNAase I (Sigma Chemical Company, St. Louis, Mo.) in Tris-EDTA (TE) (10 mM Tris(hydroxymethyl)aminomethane (Tris), 1 mM EDTA, pH 8.0, sterile) and incubating at 35° C. for at least 30 minutes. The fluorescence released from the surface of each well was quantitated with a PerSeptive Biosystems Cytofluor II microtiter plate fluorimeter (PerSeptive Biosystems, Inc., Framingham, Mass.) using the manufacturer's recommended excitation and emission filter sets for fluorescein. Each plate hybridization was performed in quadruplicate, and the data for each probe were averaged to obtain the hybridization intensity.

Labeled RNA targets specific for G3PDH and p53 were produced via T7 RNA polymerase transcription of DNA templates in the presence of fluorescein-UTP (Boehringer Mannheim Corporation, Indianapolis, Ind.), using the same method as that outlined by Affymetrix for their GeneChip™ HIV PRT sense probe array. The DNA template for G3PDH was purchased from a commercial source (Clontech, Inc., Palo Alto, Calif.). The DNA template for p53 was obtained by sub-cloning a PCR fragment from an ATCC-derived reference clone (No. 57254) of human p53 into the commercially-available PCR cloning vector pCR2.1-TOPO (Invitrogen, Inc., Carlsbad, Calif.), then linearizing the plasmid at the end of the polycloning site opposite the vector-derived T7 promoter.

Probe predictions were performed using a software application (referred to as “p5”) that was built atop Microsoft's Access relational database application, using added Visual Basic modules, the TrueDB Grid Pro 5.0 (Apex Software Corporation, Pittsburgh, Pa.) enhancement to Visual Basic, and a version of the FORTRAN application MFOLD, modified to run in a Windows NT 4.0 environment, as an ActiveX control. The Visual Basic source code for the p5 software application is found in the CD-ROM appendix to this specification. The DNA target sequence complements that were input into p5 for division into potential oligonucleotide probe sequences are listed below:

Parent Sequence Accession No.: K03256

Locus: BUNGLOB.DNA (portion of rabbit β-globin)

Length: 122

1 TTCTTCCACA TTCACCTTGC CCCACAGGGC AGTGACCGCA GACTTCTCCT CACTGGACAG SEQ ID NO:36 61 ATGCACCATT CTGTCTGTTT TGGGGGATTG CAAGTAAACA CAGTTGTGTC AAAAGCAAGT 121 GT

Parent Sequence Accession No.: M15654

Locus: HIV_PRTA.S (HIV PRT antisense; parses into probes specific for sense-strand target)

Length: 1040

1 TGTACTGTCC ATTTATCAGG ATGGAGTTCA TAACCCATCC AAAGGAATGG AGGTTCTTTC SEQ ID NO:37 61 TGATGTTTTT TGTCTGGTGT GGTAAGTCCC CACCTCAACA GATGTTGTCT CAGCTCCTCT 121 ATTTTTGTTC TATGCTGCCC TATTTCTAAG TCAGATCCTA CATACAAATC ATCCATGTAT 181 TGATAGATAA CTATGTCTGG ATTTTGTTTT TTAAAAGGCT CTAAGATTTT TGTCATGCTA 241 CTTTGGAATA TTGCTGGTGA TCCTTTCCAT CCCTGTGGAA GCACATTGTA CTGATATCTA 301 ATCCCTGGTG TCTCATTGTT TATACTAGGT ATGGTAAATG CAGTATACTT CCTGAAGTCT 361 TCATCTAAGG GAACTGAAAA ATATGCATCA CCCACATCCA GTACTGTTAC TGATTTTTTC 421 TTTTTTAACC CTGCGGGATG TGGTATTCCT AATTGAACTT CCCAGAAGTC TTGAGTTCTC 481 TTATTAAGTT CTCTGAAATC TACTAATTTT CTCCATTTAG TACTGTCTTT TTTCTTTATG 541 GCAAATACTG GAGTATTGTA TGGATTCTCA GGCCCAATTT TTGAAATTTT CCCTTCCTTT 601 TCCATTTCTG TACAAATTTC TACTAATGCT TTTATTTTTT CTTCTGTCAA TGGCCATTGT 661 TTAACTTTTG GGCCATCCAT TCCTGGCTTT AATTTTACTG GTACAGTCTC AATAGGGCTA 721 ATGGGAAAAT TTAAAGTGCA ACCAATCTGA GTCAACAGAT TTCTTCCAAT TATGTTGACA 781 GGTGTAGGTC CTACTAATAC TGTACCTATA GCTTTATGTC CACAGATTTC TATGAGTATC 841 TGATCATACT GTCTTACTTT GATAAAACCT CCAATTCCCC CTATCATTTT TGGTTTCCAT 901 CTTCCTGGCA AACTCATTTC TTCTAATACT GTATCATCTG CTCCTGTATC TAATAGAGCT 961 TCCTTTAGTT GCCCCCCTAT CTTTATTGTG ACGAGGGGTC GTTGCCAAAG AGTGATCTGA 1021 GGGAAGTTAA AGGATACAGT

Parent Sequence Accession No.: X01677

Locus: G3PDH (Clontech G3PDH template—parses into probes specific for antisense-strand target)

Length: 999

1 GAAGGTCGGA GTCAACGGAT TTGGTCGTAT TGGGCGCCTG GTCACCAGGG CTGCTTTTAA SEQ ID NO:38 61 CTCTGGTAAA GTGGATATTG TTGCCATCAA TGACCCCTTC ATTGACCTCA ACTACATGGT 121 TTACATGTTC CAATATGATT CCACCCATGG CAAATTCCAT GGCACCGTCA AGGCTGAGAA 181 CGGGAAGCTT GTCATCAATG GAAATCCCAT CACCATCTTC CAGGAGCGAG ATCCCTCCAA 241 AATCAAGTGG GGCGATGCTG GCGCTGAGTA CGTCGTGGAG TCCACTGGCG TCTTCACCAC 301 CATGGAGAAG GCTGGGGCTC ATTTGCAGGG GGGAGCCAAA AGGGTCATCA TCTCTGCCCC 361 CTCTGCTGAT GCCCCCATGT TCGTCATGGG TGTGAACCAT GAGAAGTATG ACAACAGCCT 421 CAAGATCATC AGCAATGCCT CCTGCACCAC CAACTGCTTA GCACCCCTGG CCAAGGTCAT 481 CCATGACAAC TTTGGTATCG TGGAAGGACT CATGACCACA GTCCATGCCA TCACTGCCAC 541 CCAGAAGACT GTGGATGGCC CCTCCGGGAA ACTGTGGCGT GATGGCCGCG GGGCTCTCCA 601 GAACATCATC CCTGCCTCTA CTGGCGCTGC CAAGGCTGTG GGCAAGGTCA TCCCTGAGCT 661 AGACGGGAAG CTCACTGGCA TGGCCTTCCG TGTCCCCACT GCCAACGTGT CAGTGGTGGA 721 CCTGACCTGC CGTCTAGAAA AACCTGCCAA ATATGATGAC ATCAAGAAGG TGGTGAAGCA 781 GGCGTCGGAG GGCCCCCTCA AAGGCATCCT GGGCTACACT GAGCACCAGG TGGTCTCCTC 841 TGACTTCAAC AGCGACACCC ACTCCTCCAC CTTTGACGCT GGGGCTGGCA TTGCCCTCAA 901 CGACCACTTT GTCAAGCTCA TTTCCTGGTA TGACAACGAA TTTGGCTACA GCAACAGGGT 961 GGTGGACCTC ATGGCCCACA TGCTATAGTG AGTCGTATT

Parent Sequence Accession No.: X54156

Locus: HSP53PCRa (p53 template—parses into probes specific for antisense-strand target)

Length: 1049

1 GAGGTGCGTG TTTGTGCCTG TCCTGGGAGA GACCGGCGCA CAGAGGAAGA GAATCTCCGC SEQ ID NO:39 61 AAGAAAGGGG AGCCTCACCA CGAGCTGCCC CCAGGGAGCA CTAAGCGAGC ACTGCCCAAC 121 AACACCAGCT CCTCTCCCCA GCCAAAGAAG AAACCACTGG ATGGAGAATA TTTCACCCTT 181 CAGATCCGTG GGCGTGAGCG CTTCGAGATG TTCCGAGAGC TGAATGAGGC CTTGGAACTC 241 AAGGATGCCC AGGCTGGGAA GGAGCCAGGG GGGAGCAGGG CTCACTCCAG CCACCTGAAG 301 TCCAAAAAGG GTCAGTCTAC CTCCCGCCAT AAAAAACTCA TGTTCAAGAC AGAAGGGCCT 361 GACTCAGACT GACATTCTCC ACTTCTTGTT CCCCACTGAC AGCCTCCCTC CCCCATCTCT 421 CCCTCCCCTG CCATTTTGGG TTTTGGGTCT TTGAACCCTT GCTTGCAATA GGTGTGCGTC 481 AGAAGCACCC AGGACTTCCA TTTGCTTTGT CCCGGGGCTC CACTGAACAA GTTGGCCTGC 541 ACTGGTGTTT TGTTGTGGGG AGGAGGATGG GGAGTAGGAC ATACCAGCTT AGATTTTAAG 601 GTTTTTACTG TGAGGGATGT TTGGGAGATG TAAGAAATGT TCTTGCAGTT AAGGGTTAGT 661 TTACAATCAG CCACATTCTA GGTAGGTAGG GGCCCACTTC ACCGTACTAA CCAGGGAAGC 721 TGTCCCTCAT GTTGAATTTT CTCTAACTTC AAGGCCCATA TCTGTGAAAT GCTGGCATTT 781 GCACCTACCT CACAGAGTGC ATTGTGAGGG TTAATGAAAT AATGTACATC TGGCCTTGAA 841 ACCACCTTTT ATTACATGGG GTCTAAAACT TGACCCCCTT GAGGGTGCCT GTTCCCTCTC 901 CCTCTCCCTG TTGGCTGGTG GGTTGGTAGT TTCTACAGTT GGGCAGCTGG TTAGGTAGAG 961 GGAGTTGTCA AGTCTTGCTG GCCCAGCCAA ACCCTGTCTG ACAACCTCTT GGTCGACCTT 1021 AGTACCTAAA AGGAAATCTC ACCCCATCC

The sequences indicated above, which are complements of the target sequences, were divided into overlapping oligonucleotide sequences with one nucleotide between starting positions. The oligonucleotide sequence lengths were 17 (rabbit βglobin), 20 (HIV PRT) or 25 (G3PDH; p53). The oligonucleotide sequence lengths were dictated by the probe lengths used in the experiments to which the predictions were compared. The RNA target concentrations used to calculate predicted RNA/DNA duplex melting temperatures were 100 pM (rabbit β-globin), 26.3 nM (HIV PRT) and 10 nM (G3PDH; p53). These were also dictated by experimental conditions for the comparison data. The cut-off filter used for the predicted free energy of the most stable probe sequence intramolecular structure, ΔG_(MFOLD), was ${\Delta \quad G_{MFOLD}} \geq {{- 0.4}\quad {\frac{kcal}{mole}.}}$

The filter condition used for the predicted RNA/DNA duplex melting temperature was

25° C.≦T_(m)+16.6 log([Na⁺])−T_(hyb)≦50° C.,

where T_(m) is the target concentration-dependent value of the predicted RNA/DNA duplex melting temperature before correction for salt concentration, the term “16.6 log([Na⁺])” corrects the melting temperature for salt effects, and T_(hyb) is the hybridization temperature. The values of the salt correction term and T_(hyb) have already been listed in Table 2. For convenient use within p5, the above condition was algebraically rearranged into the equivalent form

25° C.−16.6 log([Na⁺])+T_(hyb)≦T_(m)≦50° C.−16.6 log([Na⁺])+T_(hyb).

Clusters were ranked according to the number of contiguous oligonucleotide sequences that passed through the filter set (“contig” length).

Results:

The detailed analysis results for rabbit β-globin are presented in Table 3; a graphical summary of the results is shown in FIG. 4. In Table 3, values of T_(m) and ΔG_(MFOLD) that were excluded by the filter set are shown with a line through them, and table entries for contig length are shown in gray when the oligonucleotide sequence in question was not in a contig. The top 20% of the observed hybridization intensities are shown underlined.

TABLE 3 Oligonucleotide SEQ ID ΔG_(MFOLD) Contig Hybridization Intensity Position Sequence NO: T_(m)(° C.) (kcal/mole) Length (Milner et al., 1997) 1 TTCTTCCACATTCACCT 40

5.00 100 2 TCTTCCACATTCACCTT 41

5.00 130 3 CTTCCACATTCACCTTG 42

0.90 130 4 TTCCACATTCACCTTGC 43

0.50 200 5 TCCACATTCACCTTGCC 44 58.46 0.50 7 120 6 CCACATTCACCTTGCCC 45 61.10 0.50 7 180 7 CACATTCACCTTGCCCC 46 61.10 0.50 7 230 8 ACATTCACCTTGCCCCA 47 61.10 0.50 7 220 9 CATTCACCTTGCCCCAC 48 61.10 0.90 7 320 10 ATTCACCTTGCCCCACA 49 61.10 0.70 7 310 11 TTCACCTTGCCCCACAG 50 61.33 0.50 7 320 12 TCACCTTGCCCCACAGG 51 63.70

390 13 CACCTTGCCCCACAGGG 52 64.85

410 14 ACCTTGCCCCACAGGGC 53 68.01

240 15 CCTTGCCCCACAGGGCA 54 68.63

 50 16 CTTGCCCCACAGGGCAG 55 64.95

 20 17 TTGCCCCACAGGGCAGT 56 66.31

 20 18 TGCCCCACAGGGCAGTG 57 65.79

 20 19 GCCCCACAGGGCAGTGA 58 67.37

 20 20 CCCCACAGGGCAGTGAC 59 63.42

 40 21 CCCACAGGGCAGTGACC 60 63.42

 20 22 CCACAGGGCAGTGACCG 61 59.85

 20 23 CACAGGGCAGTGACCGC 62 60.14

 20 24 ACAGGGCAGTGACCGCA 63 60.14

 20 25 CAGGGCAGTGACCGCAG 64 59.76

 30 26 AGGGCAGTGACCGCAGA 65 59.83

 20 27 GGGCAGTGACCGCAGAC 66 60.22

 30 28 GGCAGTGACCGCAGACT 67 59.53

 30 29 GCAGTGACCGCAGACTT 68 57.06

 30 30 CAGTGACCGCAGACTTC 69

 40 31 AGTGACCGCAGACTTCT 70

−0.20  40 32 GTGACCGCAGACTTCTC 71 55.99 0.60 7 100 33 TGACCGCAGACTTCTCC 72 57.01 0.60 7 120 34 GACCGCAGACTTCTCCT 73 59.22 0.60 7 180 35 ACCGCAGACTTCTCCTC 74 59.28 0.60 7 210 36 CCGCAGACTTCTCCTCA 75 60.07 0.60 7 200 37 CGCAGACTTCTCCTCAC 76 56.34 0.60 7 190 38 GCAGACTTCTCCTCACT 77 57.79 0.60 7 240 39 CAGACTTCTCCTCACTG 78

0.60 240 40 AGACTTCTCCTCACTGG 79

0.00 340 41 GACTTCTCCTCACTGGA 80 55.77

340 42 ACTTCTCCTCACTGGAC 81

240 43 CTTCTCCTCACTGGACA 82 55.75

240 44 TTCTCCTCACTGGACAG 83

120 45 TCTCCTCACTGGACAGA 84

100 46 CTCCTCACTGGACAGAT 85

110 47 TCCTCACTGGACAGATG 86

 80 48 CCTCACTGGACAGATGC 87

0.00 240 49 CTCACTGGACAGATGCA 88

0.20  90 50 TCACTGGACAGATGCAC 89

0.20  30 51 CACTGGACAGATGCACC 90

0.50 100 52 ACTGGACAGATGCACCA 91

 80 53 CTGGACAGATGCACCAT 92

 90 54 TGGACAGATGCACCATT 93

 80 55 GGACAGATGCACCATTC 94

0.30 180 56 GACAGATGCACCATTCT 95

−0.10 220 57 ACAGATGCACCATTCTG 96

120 58 CAGATGCACCATTCTGT 97

120 59 AGATGCACCATTCTGTC 98

−0.10 250 60 GATGCACCATTCTGTCT 99

0.30 520 61 ATGCACCATTCTGTCTG 100

0.40 980 62 TGCACCATTCTGTCTGT 101 56.05 0.20 2 780 63 GCACCATTCTGTCTGTT 102 56.52 0.20 2 810 64 CACCATTCTGTCTGTTT 103

0.20 220 65 ACCATTCTGTCTGTTTT 104

0.20 120 66 CCATTCTGTCTGTTTTG 105

0.20 120 67 CATTCTGTCTGTTTTGG 106

0.60 160 68 ATTCTGTCTGTTTTGGG 107

1.70 310 69 TTCTGTCTGTTTTGGGG 108

1.70 250 70 TCTGTCTGTTTTGGGGG 109 55.90 1.70 2  80 71 CTGTCTGTTTTGGGGGA 110 55.91 1.40 2  30 72 TGTCTGTTTTGGGGGAT 111

0.90  50 73 GTCTGTTTTGGGGGATT 112

0.90  10 74 TCTGTTTTGGGGGATTG 113

1.10  10 75 CTGTTTTGGGGGATTGC 114

2.20  10 76 TGTTTTGGGGGATTGCA 115

1.20  10 77 GTTTTGGGGGATTGCAA 116

0.00   5 78 TTTTGGGGGATTGCAAG 117

−0.20   5 79 TTTGGGGGATTGCAAGT 118

−0.20   5 80 TTGGGGGATTGCAAGTA 119

0.00   5 81 TGGGGGATTGCAAGTAA 120

1.20   5 82 GGGGGATTGCAAGTAAA 121

1.40   5 83 GGGGATTGCAAGTAAAC 122

1.40   5 84 GGGATTGCAAGTAAACA 123

1.30   5 85 GGATTGCAAGTAAACAC 124

0.90   5 86 GATTGCAAGTAAACACA 125

0.50   5 87 ATTGCAAGTAAACACAG 126

0.50   5 88 TTGCAAGTAAACACAGT 127

0.50   5 89 TGCAAGTAAACACAGTT 128

0.30   5 90 GCAAGTAAACACAGTTG 129

0.10  10 91 CAAGTAAACACAGTTGT 130

−0.30   5 92 AAGTAAACACAGTTGTG 131

  5 93 AGTAAACACAGTTGTGT 132

  5 94 GTAAACACAGTTGTGTC 133

  5 95 TAAACACAGTTGTGTCA 134

  5 96 AAACACAGTTGTGTCAA 135

  5 97 AACACAGTTGTGTCAAA 136

  5 98 ACACAGTTGTGTCAAAA 137

 10 99 CACAGTTGTGTCAAAAG 138

 15 100 ACAGTTGTGTCAAAAGC 139

 30 101 CAGTTGTGTCAAAAGCA 140

0.20  25 102 AGTTGTGTCAAAAGCAA 141

−0.10  25 103 GTTGTGTCAAAAGCAAG 142

−0.30  20 104 TTGTGTCAAAAGCAAGT 143

−0.10 120 105 TGTGTCAAAAGCAAGTG 144

0.50  20

In FIG. 4, the hybridization intensity observed experimentally is plotted as a function of oligonucleotide starting position in the target-complementary sequence that was input into p5. The identified contigs are plotted as horizontal bars, with the contig rank (by length) shown in parentheses next to each bar. It is clear from Table 3 and FIG. 4 that the prediction algorithm identified contigs that overlap all of the “top 20%” hybridization intensity peaks observed. Iterative experimental improvement of these predictions would converge on each of the observed intensity maxima in 3-4 iterations.

Prediction worksheets for HIV PRT, G3PDH and p53 were prepared in a manner similar to that for rabbit β-globin as shown in Table 3, except that the probes were longer as indicated above and that approximately 1,000 probes were analyzed for each of these genes. The results of these analyses are shown in FIG. 5 (HIV PRT), FIG. 6 (G3PDH) and FIG. 7 (p53). In FIG. 5, data are plotted for all possible 20-mer oligonucleotide probes. In FIGS. 6 and 7, data were available for only every 10^(th)25-mer probe, and the actual data points are plotted as open diamonds.

It is clear from FIGS. 5-7 that the hybridization efficiency prediction algorithm of the present invention performed well in the task of identifying regions with observed high hybridization intensity. In each case, the 4 longest contigs point to good-to-excellent regions for experimental investigation. It should be noted that the contigs usually bracket observed intensity peaks; experimental iterative refinement would therefore be expected to converge in 2-3 iterations. By this is meant that certain oligonucleotides from the identified contigs are prepared and subjected to evaluation in actual hybridization experiments. Based on the results of such experiments, the observed signal is evaluated to determine whether the oligonucleotides are hybridizing to the left of, the right of, or on the center of a peak with respect to the graphed data. The next iteration is carried out to experimentally evaluate the hybridization efficiency of probes that are inferred to lie closer to the peak of hybridization efficiency, based on the data from the previous iteration. Iteration is continued until the signal level is deemed acceptable by the user, or the local hybridization efficiency maximum is reached (i.e. the best probe in the cluster identified by the method of the current invention has been experimentally identified). A detailed illustration of this process is shown in Example 3.

It should be noted that clusters of predictions that overlap the maxima of observed peaks of hybridization efficiency will often yield user-acceptable probes on the first iteration. Thus, the method of the present invention is much more efficient than current methods in which every potential probe is synthesized. For instance, in the HIV PRT example shown in FIG. 5, at least 3 good probes would be identified after synthesis of ˜10 test probes (i.e. statistical sampling of the 3 longest contigs). This is much more efficient than the ˜1,000 probes represented by the data in FIG. 5.

Example 2

Synopsis:

Data from a labeled RNA target hybridization to an Affymetrix GeneChip™ HIV PRT-sense probe array (GeneChip™ HIV PRT 440s, Affymetrix Corporation, Santa Clara, Calif.) were compared to the predictions of the window-averaged composite dimensionless score version of the method of the present invention.

Materials and Methods:

Data were obtained as described for the Affymetrix GeneChip™ HIV PRT-sense probe array (GeneChip™ HIV PRT 440s, Affymetrix Corporation, Santa Clara, Calif.) in Example 1. The DNA sequence (SEQ ID NO: 37) complementary to the fluorescein-labeled RNA target was divided into overlapping 20-mer oligonucleotide sequences spaced one nucleotide apart, using the prototype application p5; p5 was also used to calculate the predicted values of the RNA/DNA heteroduplex melting temperature (T_(m)) and the free energy of the most stable predicted probe intramolecular structure, ΔG_(MFOLD), as described in Example 1. The probe sequences and parameter values were then transferred to a Microsoft Excel spreadsheet, which was used to complete the predictions of efficient and inefficient probes. The weight was obtained by optimizing the performance of the algorithm with the data of Milner et al., supra, as the training data using the Microsoft® Excel® spreadsheet software. The composite score was calculated using a weight of 0.62 for the dimensionless Tm score and a weight of 0.38 for the ΔG_(MFOLD) dimensionless score. The windowed-averaging was performed using a window width of 7 and Microsoft® Excel® spreadsheet software. Finally, the oligonucleotide sequences having the top 10% of the window-averaged composite dimensionless scores were predicted to be efficient probes, while the oligonucleotide sequences having the bottom 10% of the window-averaged composite dimensionless scores were predicted to be inefficient probes.

Results:

The calculated parameters and scores are shown in Table 4; the algorithm predictions are also shown diagrammatically in FIG. 8. In Table 4, window-averaged composite score values that were in the top 10% of the distribution of values are shown in bold type, values that were in the bottom 10% are shown in italics, and all other values are shown with a line through them. It is clear from both Table 4 and FIG. 8 that the window-averaged composite dimensionless score embodiment of the current invention correctly predicted both efficient and inefficient hybridization probes for HIV PRT sense-strand RNA. As in Example 1, statistical sampling of contiguous stretches of predicted “good” probes would lead to convergence of the design process to the best probes in each region in 2-4 design iterations.

TABLE 4 Window- ≢G_(MFOLD) Averaged HIV PRT p5 Probe SEQ ID RNA/DNA (kcal/ T_(m) ΔG_(MFOLD) Composite Composite GeneChip ™ Position DNA Probe Sequence NO: T_(m) (° C.) mole @ 35° C.) Score Score Score Score Data  1 GTACTGTCCATTTATCAGGA 145 64.16 −0.10 0.557 −0.199 0.269 1152.2  2 TACTGTCCATTTATCAGGAT 146 60.91 −0.40 0.080 −0.460 −0.125 1040.7  3 ACTGTCCATTTATCAGGATG 147 61.41 −0.90 0.152 −0.895 −0.246 291.9  4 CTGTCCATTTATCAGGATGG 148 63.46 −0.90 0.453 −0.895 −0.059 ———−0.168 221.8  5 TGTCCATTTATCAGGATGGA 149 62.82 −0.90 0.360 −0.895 −0.117 ———−0.281 148.3  6 GTCCATTTATCAGGATGGAG 150 63.15 −1.90 0.408 −1.764 −0.418 ———−0.308 84.6  7 TCCATTTATCAGGATGGAGT 151 63.15 −2.10 0.408 −1.938 −0.484 ———−0.252 128.7  8 CCATTTATCAGGATGGAGTT 152 62.03 −1.90 0.245 −1.764 −0.519 ———−0.242 94.6  9 CATTTATCAGGATGGAGTTC 153 59.53 −0.60 −0.122 −0.634 −0.317 ———−0.236 157.5  10 ATTTATCAGGATGGAGTTCA 154 59.53 0.80 −0.122 0.583 0.146 ———−0.227 316.9  11 TTTATCAGGATGGAGTTCAT 155 59.53 0.40 −0.122 0.236 0.014 ———−0.194 360.2  12 TTATCAGGATGGAGTTCATA 156 58.58 0.40 −0.262 0.236 −0.073 ———−0.105 403.8  13 TATCAGGATGGAGTTCATAA 157 56.21 0.20 −0.609 0.062 −0.354 ———−0.014 382.5  14 ATCAGGATGGAGTTCATAAC 158 57.34 0.20 −0.444 0.062 −0.252 ———−0.004 324.4  15 TCAGGATGGAGTTCATAACC 159 61.25 0.20 0.129 0.062 0.104 ———−0.035 320.5  16 CAGGATGGAGTTCATAACCC 160 63.57 0.20 0.470 0.062 0.315 ———−0.101 238.9  17 AGGATGGAGTTCATAACCCA 161 63.57 −0.10 0.470 −0.199 0.216 ———−0.157 202.3  18 GGATGGAGTTCATAACCCAT 162 63.34 −1.30 0.436 −1.243 −0.202 ———−0.120 113.6  19 GATGGAGTTCATAACCCATC 163 62.24 −2.00 0.275 −1.851 −0.533 ———−0.099 97.7  20 ATGGAGTTCATAACCCATCC 164 64.62 −3.30 0.624 −2.982 −0.746 ———−0.100 143.3  21 TGGAGTTCATAACCCATCCC 165 68.18 −2.00 1.146 −1.851 0.007 ———−0.109 484.6  22 GGAGTTCATAACCCATCCCA 166 69.39 −1.60 1.324 −1.504 0.249 ———−0.058 857.6  23 GAGTTCATAACCCATCCCAA 167 64.93 −0.20 0.670 −0.286 0.307 ——— 0.053 991.4  24 AGTTCATAACCCATCCCAAA 168 61.82 0.20 0.213 0.062 0.155 ——— 0.173 907.0  25 GTTCATAACCCATCCCAAAG 169 61.82 0.20 0.213 0.062 0.155 ——— 0.137 887.9  26 TTCATAACCCATCCCAAAGG 170 61.36 0.60 0.145 0.410 0.246 ——— 0.053 1015.3  27 TCATAACCCATCCCAAAGGA 171 62.21 −0.10 0.270 −0.199 0.092 ———0.040 279.7  28 CATAACCCATCCCAAAGGAA 172 59.26 −0.30 −0.163 −0.373 −0.243 ———−0.124 210.7  29 ATAACCCATCCCAAAGGAAT 173 58.19 −0.30 −0.320 −0.373 −0.340 ———−0.204 179.9  30 TAACCCATCCCAAAGGAATG 174 58.13 −0.30 −0.328 −0.373 −0.345 ———−0.309 91.8  31 AACCCATCCCAAAGGAATGG 175 60.78 −1.30 0.061 −1.243 −0.435 ———−0.412 44.6  32 ACCCATCCCAAAGGAATGGA 176 63.69 −2.00 0.487 −1.551 −0.401 ———−0.488 42.9  33 CCCATCCCAAAGGAATGGAG 177 63.40 −2.20 0.445 −2.025 −0.494 ———−0.542 45.0  34 CCATCCCAAAGGAATGGAGG 178 62.34 −2.30 0.290 −2.112 −0.623 ———−0.579 45.3  35 CATCCCAAAGGAATGGAGGT 179 61.72 −2.60 0.199 −2.373 −0.778 ———−0.587 47.9  36 ATCCCAAAGGAATGGAGGTT 180 60.90 −2.20 0.079 −2.025 −0.721 ———−0.580 49.2  37 TCCCAAAGGAATGGAGGTTC 181 62.24 −2.20 0.274 −2.025 −0.600 ———−0.585 74.2  38 CCCAAAGGAATGGAGGTTCT 182 62.71 −2.00 0.344 −1.851 −0.490 ———−0.572 125.5  39 CCAAAGGAATGGAGGTTCTT 183 59.47 −0.70 −0.132 −0.721 −0.356 ———−0.485 183.3  40 CAAAGGAATGGAGGTTCTTT 184 56.10 −0.30 −0.627 −0.373 −0.530 ———−0.380 261.4  41 AAAGGAATGGAGGTTCTTTC 185 56.11 −0.30 −0.625 −0.373 −0.529 ———−0.277 518.3  42 AAGGAATGGAGGTTCTTTCT 186 60.05 −0.30 −0.046 −0.373 −0.170 ———−0.206 716.5  43 AGGAATGGAGGTTCTTTCTG 187 62.09 −0.30 0.253 −0.373 0.015 ———−0.164 1056.0  44 GGAATGGAGGTTCTTTCTGA 188 63.23 −0.30 0.420 −0.373 0.119 ———−0.025 1084.3  45 GAATGGAGGTTCTTTCTGAT 189 60.56 0.10 0.028 −0.025 0.008 ——— 0.119 1241.1  46 AATGGAGGTTCTTTCTGATG 190 59.12 0.30 −0.183 0.149 −0.057 ——— 0.217 1278.8  47 ATGGAGGTTCTTTCTGATGT 191 64.58 0.30 0.618 0.149 0.440 ——— 0.258 1616.0  48 TGGAGGTTCTTTCTGATGTT 192 64.98 0.30 0.677 0.149 0.476 ——— 0.270 1677.5  49 GGAGGTTCTTTCTGATGTTT 193 65.49 0.30 0.751 0.149 0.522 ——— 0.300 1963.1  50 GAGGTTCTTTCTGATGTTTT 194 63.04 0.30 0.392 0.149 0.300 ——— 0.301 2126.1  51 AGGTTCTTTCTGATGTTTTT 195 61.97 0.30 0.235 0.149 0.202 ——— 0.231 2143.3  52 GGTTCTTTCTGATGTTTTTT 196 62.11 0.30 0.256 0.149 0.215 ——— 0.180 3540.6  53 GTTCTTTCTGATGTTTTTTG 197 59.21 0.30 −0.170 0.149 −0.049 ——— 0.164 1728.7  54 TTCTTTCTGATGTTTTTTGT 198 59.21 0.30 −0.170 0.149 −0.049 ——— 0.151 1364.3  55 TCTTTCTGATGTTTTTTGTC 199 60.35 0.50 −0.002 0.323 0.121 ——— 0.183 1788.4  56 CTTTCTGATGTTTTTTGTCT 200 60.96 1.20 0.086 0.931 0.407 ——— 0.253 2670.9  57 TTTCTGATGTTTTTTGTCTG 201 58.76 1.20 −0.235 0.931 0.208 ——— 0.338 3336.2  58 TTCTGATGTTTTTTGTCTGG 202 61.17 1.20 0.118 0.931 0.427 ——— 0.440 6683.6  59 TCTGATGTTTTTTGTCTGGT 203 64.20 1.20 0.562 0.931 0.702 ——— 0.537 10227.0  60 CTGATGTTTTTTGTCTGGTG 204 62.51 1.20 0.315 0.931 0.549 ——— 0.625 10965.0  61 TGATGTTTTTTGTCTGGTGT 205 63.80 1.20 0.504 0.931 0.666 ——— 0.778 11133.0  62 GATGTTTTTTGTCTGGTGTG 206 63.80 1.60 0.504 1.279 0.798  0.894 11503.0  63 ATGTTTTTTGTCTGGTGTGG 207 65.18 1.90 0.705 1.540 1.023  0.894 9492.8  64 TGTTTTTTGTCTGGTGTGGT 208 68.78 1.70 1.234 1.366 1.284  0.914 10704.0  65 GTTTTTTGTCTGGTGTGGTA 209 68.28 1.70 1.161 1.366 1.239  0.933 10741.0  66 TTTTTTGTCTGGTGTGGTAA 210 62.37 1.70 0.294 1.366 0.701  0.950 9187.5  67 TTTTTGTCTGGTGTGGTAAG 211 62.23 1.70 0.273 1.366 0.689  0.941 7871.0  68 TTTTGTCTGGTGTGGTAAGT 212 65.28 1.20 0.721 0.931 0.801  0.921 7209.1  69 TTTGTCTGGTGTGGTAAGTC 213 66.56 1.20 0.908 0.931 0.917  0.959 8052.3  70 TTGTCTGGTGTGGTAAGTCC 214 70.25 0.30 1.449 0.149 0.955  1.022 7230.6  71 TGTCTGGTGTGGTAAGTCCC 215 73.77 −0.10 1.966 −0.199 1.143  0.998 6809.5  72 GTCTGGTGTGGTAAGTCCCC 216 77.74 −0.10 2.549 −0.199 1.504  0.913 7442.8  73 TCTGGTGTGGTAAGTCCCCA 217 75.28 −0.50 2.187 −0.547 1.148 ——— 0.824 2627.7  74 CTGGTGTGGTAAGTCCCCAC 218 74.18 −2.10 2.026 −1.938 0.519 ——— 0.781 1315.0  75 TGGTGTGGTAAGTCCCCACC 219 75.80 −3.50 2.263 −3.156 0.204 ——— 0.680 4182.3  76 GGTGTGGTAAGTCCCCACCT 220 77.89 −3.80 2.571 −3.417 0.296 ——— 0.518 474.7  77 GTGTGGTAAGTCCCCACCTC 221 77.05 −2.50 2.448 −2.286 0.649 ——— 0.429 682.4  78 TGTGGTAAGTCCCCACCTCA 222 74.71 −2.50 2.105 −2.286 0.436 ——— 0.465 679.1  79 GTGGTAAGTCCCCACCTCAA 223 72.54 −2.10 1.785 −1.938 0.370 ——— 0.584 924.0  80 TGGTAAGTCCCCACCTCAAC 224 69.94 −0.90 1.404 −0.895 0.531 ——— 0.667 835.5  81 GGTAAGTCCCCACCTCAACA 225 71.14 −0.50 1.580 −0.547 0.772 ——— 0.687 1213.6  82 GTAAGTCCCCACCTCAACAG 226 68.97 0.90 1.262 0.670 1.037 ——— 0.763 1106.1  83 TAAGTCCCCACCTCAACAGA 227 67.18 0.90 0.999 0.670 0.874  0.872 1009.0  84 AAGTCCCCACCTCAACAGAT 228 67.68 0.50 1.073 0.323 0.788  0.908 1656.2  85 AGTCCCCACCTCAACAGATG 229 69.68 0.50 1.366 0.323 0.970 ——— 0.831 2178.3  86 GTCCCCACCTCAACAGATGT 230 72.56 0.20 1.789 0.062 1.132 ——— 0.679 2567.0  87 TCCCCACCTCAACAGATGTT 231 69.77 −0.10 1.379 −0.199 0.779 ——— 0.522 3000.5  88 CCCCACCTCAACAGATGTTG 232 68.19 −1.30 1.148 −1.243 0.240 ——— 0.354 2025.4  89 CCCACCTCAACAGATGTTGT 233 67.78 −2.00 1.087 −1.851 −0.030 ——— 0.164 429.2  90 CCACCTCAACAGATGTTGTC 234 65.65 −2.00 0.775 −1.851 −0.223 ———−0.041 157.9  91 CACCTCAACAGATGTTGTCT 235 63.85 −2.00 0.511 −1.851 −0.387 ———−0.244 135.3  92 ACCTCAACAGATGTTGTCTC 236 64.11 −2.00 0.549 −1.851 −0.363 ———−0.339 330.8  93 CCTCAACAGATGTTGTCTCA 237 64.77 −2.00 0.646 −1.851 −0.303 ———−0.370 900.0  94 CTCAACAGATGTTGTCTCAG 238 61.08 −2.00 0.104 −1.851 −0.639 ———−0.300 1177.0  95 TCAACAGATGTTGTCTCAGC 239 63.40 −2.00 0.444 −1.851 −0.428 ———−0.117 795.1  96 CAACAGATGTTGTCTCAGCT 240 63.91 −1.60 0.520 −1.504 −0.249 ——— 0.081 889.2  97 AACAGATGTTGTCTCAGCTC 241 64.19 −0.10 0.560 −0.199 0.272 ——— 0.287 1703.6  98 ACAGATGTTGTCTCAGCTCC 242 70.61 0.00 1.503 −0.112 0.889 ——— 0.598 3115.2  99 CAGATGTTGTCTCAGCTCCT 243 72.08 0.00 1.719 −0.112 1.023  0.847 4445.0 100 AGATGTTGTCTCAGCTCCTC 244 72.66 0.20 1.803 0.062 1.141  1.070 6762.8 101 GATGTTGTCTCAGCTCCTCT 245 74.49 0.90 2.071 0.670 1.539  1.227 8845.0 102 ATGTTGTCTCAGCTCCTCTA 246 72.38 0.80 1.763 0.583 1.314  1.253 9010.6 103 TGTTGTCTCAGCTCCTCTAT 247 72.38 0.80 1.763 0.583 1.314  1.260 19941.0 104 GTTGTCTCAGCTCCTCTATT 248 72.97 0.80 1.849 0.583 1.368  1.257 12577.0 105 TTGTCTCAGCTCCTCTATTT 249 69.70 0.80 1.369 0.583 1.071  1.149 7503.3 106 TGTCTCAGCTCCTCTATTTT 250 69.70 0.80 1.369 0.583 1.071  1.098 7033.8 107 GTCTCAGCTCCTCTATTTTT 251 70.26 0.80 1.451 0.583 1.121  1.024 8276.7 108 TCTCAGCTCCTCTATTTTTG 252 66.57 0.80 0.910 0.583 0.786  0.942 2899.0 109 CTCAGCTCCTCTATTTTTGT 253 68.39 0.80 1.177 0.583 0.952  0.923 2935.0 110 TCAGCTCCTCTATTTTTGTT 254 66.69 0.80 0.927 0.583 0.796  0.930 1512.8 111 CAGCTCCTCTATTTTTGTTC 255 66.69 0.80 0.927 0.583 0.796  0.872 1708.8 112 AGCTCCTCTATTTTTGTTCT 256 67.52 1.00 1.050 0.757 0.939  0.833 1977.3 113 GCTCCTCTATTTTTGTTCTA 257 66.63 1.80 0.919 1.453 1.122 ——— 0.809 2114.8 114 CTCCTCTATTTTTGTTCTAT 258 62.13 1.80 0.259 1.453 0.713 ——— 0.766 1527.3 115 TCCTCTATTTTTGTTCTATG 259 59.97 1.80 0.058 1.453 0.516 ——— 0.695 1536.8 116 CCTCTATTTTTGTTCTATGC 260 62.84 1.80 0.363 1.453 0.777 ——— 0.642 1824.5 117 CTCTATTTTTGTTCTATGCT 261 60.87 1.50 0.074 1.192 0.499 ——— 0.588 1169.2 118 TCTATTTTTGTTCTATGCTG 262 58.71 1.50 −0.244 1.192 0.302 ——— 0.649 683.7 119 CTATTTTTGTTCTATGCTGC 263 61.60 1.50 0.181 1.192 0.565 ——— 0.765 1306.8 120 TATTTTTGTTCTATGCTGCC 264 63.53 1.50 0.464 1.192 0.741 ——— 0.831 2523.6 121 ATTTTTGTTCTATGCTGCCC 265 67.96 1.50 1.113 1.192 1.143  0.931 6682.0 122 TTTTTGTTCTATGCTGCCCT 266 69.96 1.50 1.407 1.192 1.325  1.060 9417.4 123 TTTTGTTCTATGCTGCCCTA 267 69.01 1.50 1.267 1.192 1.239  1.151 10339.0 124 TTTGTTCTATGCTGCCCTAT 268 68.62 1.50 1.210 1.192 1.203  1.254 10750.0 125 TTGTTCTATGCTGCCCTATT 269 68.62 1.50 1.210 1.192 1.203  1.282 11180.0 126 TGTTCTATGCTGCCCTATTT 270 68.62 1.50 1.210 1.192 1.203  1.271 11060.0 127 GTTCTATGCTGCCCTATTTC 271 70.37 1.80 1.468 1.453 1.462  1.221 16074.0 128 TTCTATGCTGCCCTATTTCT 272 69.00 1.80 1.266 1.453 1.337  1.144 9183.8 129 TCTATGCTGCCCTATTTCTA 273 68.05 1.80 1.127 1.453 1.251  1.082 8617.8 130 CTATGCTGCCCTATTTCTAA 274 64.38 1.70 0.589 1.366 0.884  1.040 7286.8 131 TATGCTGCCCTATTTCTAAG 275 62.71 1.50 0.344 1.192 0.666  0.978 3642.4 132 ATGCTGCCCTATTTCTAAGT 276 66.39 0.80 0.883 0.583 0.769  0.883 3799.7 133 TGCTGCCCTATTTCTAAGTC 277 67.95 0.80 1.112 0.583 0.911 ——— 0.749 3408.3 134 GCTGCCCTATTTCTAAGTCA 278 69.25 0.80 1.303 0.583 1.030 ——— 0.644 4017.4 135 CTGCCCTATTTCTAAGTCAG 279 65.26 0.80 0.718 0.583 0.667 ——— 0.536 2197.2 136 TGCCCTATTTCTAAGTCAGA 280 64.63 −0.10 0.626 −0.199 0.312 ——— 0.412 1125.0 137 GCCCTATTTCTAAGTCAGAT 281 64.73 −0.60 0.639 −0.634 0.156 ——— 0.244 1306.3 138 CCCTATTTCTAAGTCAGATC 282 61.98 −0.60 0.236 −0.634 −0.094 ——— 0.024 1019.5 139 CCTATTTCTAAGTCAGATCC 283 61.98 −0.60 0.236 −0.634 −0.094 ———−0.129 1852.3 140 CTATTTCTAAGTCAGATCCT 284 60.05 −0.60 −0.046 −0.634 −0.270 ———−0.214 3159.3 141 TATTTCTAAGTCAGATCCTA 285 57.43 −0.60 −0.430 −0.634 −0.508 ———−0.281 2604.8 142 ATTTCTAAGTCAGATCCTAC 286 58.59 −0.60 −0.261 −0.634 −0.402 ———−0.315 3986.1 143 TTTCTAAGTCAGATCCTACA 287 59.91 −0.60 −0.068 −0.634 −0.283 ———−0.285 4500.7 144 TTCTAAGTCAGATCCTACAT 288 59.55 −0.60 −0.120 −0.634 −0.315 ———−0.233 4754.5 145 TCTAAGTCAGATCCTACATA 289 58.62 −0.40 −0.257 −0.460 −0.334 ———−0.165 3802.1 146 CTAAGTCAGATCCTACATAC 290 57.80 1.20 −0.377 0.931 0.120 ———−0.111 5069.4 147 TAAGTCAGATCCTACATACA 291 57.13 1.30 −0.476 1.018 0.092 ———−0.059 3965.2 148 AAGTCAGATCCTACATACAA 292 55.78 1.30 −0.673 1.018 −0.030 ———−0.031 3862.3 149 AGTCAGATCCTACATACAAA 293 55.78 1.30 −0.673 1.018 −0.030 ———−0.020 2868.9 150 GTCAGATCCTACATACAAAT 294 55.62 1.70 −0.697 1.366 0.087 ———−0.089 3542.9 151 TCAGATCCTACATACAAATC 295 54.02 1.50 −0.932 1.192 −0.125 ———−0.122 2477.1 152 CAGATCCTACATACAAATCA 296 54.07 1.10 −0.924 0.844 −0.252 ———−0.091 2522.4 153 AGATCCTACATACAAATCAT 297 52.83 1.10 −1.106 0.844 −0.365 ———−0.045 2554.6 154 GATCCTACATACAAATCATC 298 53.87 1.50 −0.953 1.192 −0.138 ———−0.031 3580.0 155 ATCCTACATACAAATCATCC 299 56.33 1.80 −0.591 1.453 0.185 ———−0.067 5937.7 156 TCCTACATACAAATCATCCA 300 57.54 1.80 −0.415 1.453 0.295 ———−0.111 4606.7 157 CCTACATACAAATCATCCAT 301 56.32 1.80 −0.594 1.453 0.184 ———−0.159 4877.2 158 CTACATACAAATCATCCATG 302 52.68 1.10 −1.128 0.844 −0.379 ———−0.278 2608.6 159 TACATACAAATCATCCATGT 303 53.56 0.30 −0.999 0.149 −0.563 ———−0.469 1491.7 160 ACATACAAATCATCCATGTA 304 53.56 −0.10 −0.999 −0.199 −0.695 ———−0.644 1364.3 161 CATACAAATCATCCATGTAT 305 53.07 −0.80 −1.071 −0.808 −0.971 −0.751 1089.8 162 ATACAAATCATCCATGTATT 306 52.11 −1.10 −1.211 −1.069 −1.157 −0.818 1008.6 163 TACAAATCATCCATGTATTG 307 52.08 −0.40 −1.215 −0.460 −0.928 −0.891 624.8 164 ACAAATCATCCATGTATTGA 308 53.86 0.20 −0.955 0.062 −0.568 −0.921 535.8 165 CAAATCATCCATGTATTGAT 309 53.36 −0.50 −1.027 −0.547 −0.845 −0.860 3019.6 166 AAATCATCCATGTATTGATA 310 51.57 −0.70 −1.291 −0.721 −1.074 −0.753 214.0 167 AATCATCCATGTATTGATAG 311 53.47 −0.70 −1.012 −0.721 −0.901 ———−0.685 212.7 168 ATCATCCATGTATTGATAGA 312 56.66 −0.50 −0.543 −0.547 −0.545 ———−0.709 165.2 169 TCATCCATGTATTGATAGAT 313 56.66 −0.10 −0.543 −0.199 −0.412 ———−0.686 166.0 170 CATCCATGTATTGATAGATA 314 54.80 0.30 −0.817 0.149 −0.450 ———−0.622 151.0 171 ATCCATGTATTGATAGATAA 315 51.69 0.30 −1.273 0.149 −0.733 ———−0.621 101.8 172 TCCATGTATTGATAGATAAC 316 52.19 0.30 −1.199 0.149 −0.687 ———−0.721 84.0 173 CCATGTATTGATAGATAACT 317 52.89 0.30 −1.097 0.149 −0.623 −0.850 130.3 174 CATGTATTGATAGATAACTA 318 48.47 0.70 −1.746 0.496 −0.894 −0.937 67.8 175 ATGTATTGATAGATAACTAT 319 47.12 0.00 −1.944 −0.112 −1.248 −1.006 65.7 176 TGTATTGATAGATAACTATG 320 47.11 −0.20 −1.945 −0.286 −1.315 −1.048 90.0 177 GTATTGATAGATAACTATGT 321 49.90 −0.20 −1.536 −0.286 −1.061 −1.099 125.9 178 TATTGATAGATAACTATGTC 322 48.24 −0.20 −1.779 −0.286 −1.212 −1.083 132.6 179 ATTGATAGATAACTATGTCT 323 50.78 −0.20 −1.407 −0.286 −0.981 −0.998 167.4 180 TTGATAGATAACTATGTCTG 324 50.75 −0.20 −1.411 −0.286 −0.984 −0.916 219.0 181 TGATAGATAACTATGTCTGG 325 53.01 −0.20 −1.080 −0.286 −0.778 −0.866 722.6 182 GATAGATAACTATGTCTGGA 326 54.36 −0.20 −0.881 −0.286 −0.655 −0.774 825.1 183 ATAGATAACTATGTCTGGAT 327 53.04 −0.10 −1.074 −0.199 −0.742 ———−0.679 844.4 184 TAGATAACTATGTCTGGATT 328 53.37 −0.10 −1.027 −0.199 −0.712 ———−0.569 912.6 185 AGATAACTATGTCTGGATTT 329 54.27 0.10 −0.895 −0.025 −0.565 ———−0.449 1301.8 186 GATAACTATGTCTGGATTTT 330 54.43 0.80 −0.870 0.583 −0.318 ———−0.335 1367.4 187 ATAACTATGTCTGGATTTTG 331 53.08 1.50 −1.070 1.192 −0.210 ———−0.177 1284.2 188 TAACTATGTCTGGATTTTGT 332 56.05 1.50 −0.634 1.192 0.060 ———−0.026 1162.5 189 AACTATGTCTGGATTTTGTT 333 56.97 1.50 −0.499 1.192 0.144 ——— 0.081 1396.7 190 ACTATGTCTGGATTTTGTTT 334 59.38 1.50 −0.145 1.192 0.363 ——— 0.176 1348.3 191 CTATGTCTGGATTTTGTTTT 335 59.16 1.50 −0.177 1.192 0.343 ——— 0.261 1092.8 192 TATGTCTGGATTTTGTTTTT 336 57.45 1.50 −0.428 1.192 0.188 ——— 0.234 912.6 193 ATGTCTGGATTTTGTTTTTT 337 58.41 1.70 −0.287 1.368 0.341 ——— 0.123 994.3 194 TGTCTGGATTTTGTTTTTTA 338 57.81 2.00 −0.375 1.627 0.386 ———−0.079 840.7 195 GTCTGGATTTTGTTTTTTAA 339 55.82 1.00 −0.667 0.757 −0.126 ———−0.311 941.9 196 TCTGGATTTTGTTTTTTAAA 340 50.98 0.80 −1.377 0.583 −0.632 ———−0.488 84.9 197 CTGGATTTTGTTTTTTAAAA 341 48.16 0.30 −1.790 0.149 −1.054 ———−0.670 78.6 198 TGGATTTTGTTTTTTAAAAG 342 46.41 0.10 −2.048 −0.025 −1.279 −0.851 93.2 199 GGATTTTGTTTTTTAAAAGG 343 48.87 0.10 −1.686 −0.025 −1.055 −0.933 56.0 200 GATTTTGTTTTTTAAAAGGC 344 50.22 0.10 −1.488 −0.025 −0.932 −0.912 49.9 201 ATTTTGTTTTTTAAAAGGCT 345 50.84 0.10 −1.397 −0.025 −0.876 −0.843 55.0 202 TTTTGTTTTTTAAAAGGCTC 346 52.03 0.30 −1.223 0.149 −0.702 −0.768 64.6 203 TTTGTTTTTTAAAAGGCTCT 347 53.64 0.50 −0.987 0.323 −0.489 ———−0.724 162.8 204 TTGTTTTTTAAAAGGCTCTA 348 52.76 0.50 −1.115 0.323 −0.569 ———−0.706 265.8 205 TGTTTTTTAAAAGGCTCTAA 349 50.71 0.50 −1.417 0.323 −0.756 ———−0.677 288.5 206 GTTTTTTAAAAGGCTCTAAG 350 50.86 0.50 −1.395 0.323 −0.742 ———−0.672 548.4 207 TTTTTTAAAAGGCTCTAAGA 351 49.40 0.70 −1.609 0.496 −0.809 ———−0.698 524.7 208 TTTTTAAAAGGCTCTAAGAT 352 49.11 1.20 −1.651 0.931 −0.670 −0.746 937.9 209 TTTTAAAAGGCTCTAAGATT 353 49.11 1.20 −1.651 0.931 −0.670 −0.790 1440.3 210 TTTAAAAGGCTCTAAGATTT 354 49.11 1.20 −1.651 0.931 −0.670 −0.820 1633.3 211 TTAAAAGGCTCTAAGATTTT 355 49.11 0.50 −1.651 0.323 −0.901 −0.735 1987.4 212 TAAAAGGCTCTAAGATTTTT 356 49.11 0.00 −1.651 −0.112 −1.067 ———−0.627 1792.3 213 AAAAGGCTCTAAGATTTTTG 357 49.63 0.20 −1.575 0.062 −0.953 ———−0.495 2218.9 214 AAAGGCTCTAAGATTTTTGT 358 54.13 1.20 −0.914 0.931 −0.213 ———−0.365 2371.4 215 AAGGCTCTAAGATTTTTGTC 359 57.38 1.20 −0.439 0.931 0.082 ———−0.238 3308.9 216 AGGCTCTAAGATTTTTGTCA 360 60.78 0.80 0.061 0.583 0.260 ———−0.087 4070.5 217 GGCTCTAAGATTTTTGTCAT 361 60.56 0.80 0.028 0.583 0.239 ——— 0.048 5394.5 218 GCTCTAAGATTTTTGTCATG 362 57.81 0.80 −0.376 0.583 −0.011 ——— 0.051 2025.5 219 CTCTAAGATTTTTGTCATGC 363 57.81 0.80 −0.376 0.583 −0.011 ———−0.006 1741.9 220 TCTAAGATTTTTGTCATGCT 364 57.81 0.80 −0.376 0.583 −0.011 ———−0.065 1707.6 221 CTAAGATTTTTGTCATGCTA 365 55.87 0.80 −0.660 0.583 −0.187 ———−0.089 1783.0 222 TAAGATTTTTGTCATGCTAC 366 54.43 0.80 −0.872 0.583 −0.319 ———−0.076 3131.4 223 AAGATTTTTGTCATGCTACT 367 56.99 0.60 −0.495 0.410 −0.151 ———−0.082 4892.5 224 AGATTTTTGTCATGCTACTT 368 59.39 0.60 −0.144 0.410 0.067 ———−0.053 5856.4 225 GATTTTTGTCATGCTACTTT 369 59.54 0.60 −0.122 0.410 0.080 ——— 0.015 6439.0 226 ATTTTTGTCATGCTACTTTG 370 58.09 0.60 −0.334 0.410 −0.051 ——— 0.069 5820.3 227 TTTTTGTCATGCTACTTTGG 371 60.78 0.60 0.060 0.410 0.193 ——— 0.095 5189.6 228 TTTTGTCATGCTACTTTGGA 372 61.79 0.60 0.209 0.410 0.285 ——— 0.079 4721.7 229 TTTGTCATGCTACTTTGGAA 373 59.35 0.60 −0.149 0.410 0.063 ——— 0.075 4221.0 230 TTGTCATGCTACTTTGGAAT 374 59.00 0.60 −0.200 0.410 0.032 ——— 0.056 4279.0 231 TGTCATGCTACTTTGGAATA 375 58.10 0.60 −0.333 0.410 −0.051 ——— 0.004 4102.0 232 GTCATGCTACTTTGGAATAT 376 58.16 0.90 −0.324 0.670 0.054 ———−0.022 5069.8 233 TCATGCTACTTTGGAATATT 377 55.52 0.90 −0.711 0.670 −0.186 ———−0.015 2407.9 234 CATGCTACTTTGGAATATTG 378 54.23 1.30 −0.900 1.018 −0.171 ——— 0.016 2443.0 235 ATGCTACTTTGGAATATTGC 379 56.90 1.40 −0.508 1.105 0.105 ——— 0.058 2324.3 236 TGCTACTTTGGAATATTGCT 380 58.82 0.90 −0.227 0.670 0.114 ——— 0.099 1894.1 237 GCTACTTTGGAATATTGCTG 381 58.82 1.30 −0.227 1.018 0.246 ——— 0.180 2363.8 238 CTACTTTGGAATATTGCTGG 382 57.35 1.70 −0.443 1.366 0.244 ——— 0.270 1363.0 239 TACTTTGGAATATTGCTGGT 383 58.39 1.70 −0.290 1.366 0.339 ——— 0.299 1217.5 240 ACTTTGGAATATTGCTGGTG 384 58.88 1.70 −0.217 1.366 0.384 ——— 0.340 1621.8 241 CTTTGGAATATTGCTGGTGA 385 59.64 1.70 −0.106 1.366 0.453 ——— 0.346 1438.2 242 TTTGGAATATTGCTGGTGAT 386 57.72 1.80 −0.388 1.453 0.311 ——— 0.345 1608.0 243 TTGGAATATTGCTGGTGATC 387 58.73 1.80 −0.241 1.453 0.403 ——— 0.302 2334.6 244 TGGAATATTGCTGGTGATCC 388 62.18 0.50 0.266 0.323 0.288 ——— 0.241 3776.7 245 GGAATATTGCTGGTGATCCT 389 64.19 −0.20 0.561 −0.286 0.239 ——— 0.216 5648.7 246 GAATATTGCTGGTGATCCTT 390 61.99 −0.20 0.238 −0.286 0.039 ——— 0.261 5358.8 247 AATATTGCTGGTGATCCTTT 391 61.03 −0.20 0.097 −0.286 −0.049 ——— 0.316 5517.2 248 ATATTGCTGGTGATCCTTTC 392 64.63 −0.20 0.625 −0.286 0.279 ——— 0.368 6246.4 249 TATTGCTGGTGATCCTTTCC 393 68.48 −0.20 1.190 −0.286 0.629 ——— 0.444 9975.1 250 ATTGCTGGTGATCCTTTCCA 394 70.22 −0.20 1.446 −0.286 0.788 ——— 0.599 11990.0 251 TTGCTGGTGATCCTTTCCAT 395 70.22 −0.60 1.446 −0.634 0.655 ——— 0.756 11543.0 252 TGCTGGTGATCCTTTCCATC 396 71.48 −0.60 1.631 −0.634 0.770  0.862 14125.0 253 GCTGGTGATCCTTTCCATCC 397 75.32 −0.60 2.193 −0.634 1.119  0.936 23489.0 254 CTGGTGATCCTTTCCATCCC 398 74.58 −0.60 2.085 −0.634 1.052  1.022 15975.0 255 TGGTGATCCTTTCCATCCCT 399 74.58 −0.70 2.085 −0.721 1.019  1.082 16053.0 256 GGTGATCCTTTCCATCCCTG 400 74.58 −0.30 2.085 −0.373 1.151  1.136 19205.0 257 GTGATCCTTTCCATCCCTGT 401 75.40 0.20 2.206 0.062 1.391  1.080 17872.0 258 TGATCCTTTCCATCCCTGTG 402 71.89 0.20 1.691 0.062 1.072  0.955 12871.0 259 GATCCTTTCCATCCCTGTGG 403 74.58 −0.30 2.085 −0.373 1.151 ——— 0.809 8792.7 260 ATCCTTTCCATCCCTGTGGA 404 74.58 −1.60 2.085 −1.504 0.721 ——— 0.653 5609.6 261 TCCTTTCCATCCCTGTGGAA 405 72.27 −2.60 1.746 −2.373 0.181 ——— 0.451 3018.0 262 CCTTTCCATCCCTGTGGAAG 406 71.00 −2.80 1.559 −2.547 −0.001 ——— 0.308 1802.6 263 CTTTCCATCCCTGTGGAAGC 407 71.60 −2.80 1.648 −2.547 0.054 ——— 0.205 1074.0 264 TTTCCATCCCTGTGGAAGCA 408 70.81 −2.80 1.532 −2.547 −0.018 ——— 0.120 1132.5 265 TTCCATCCCTGTGGAAGCAC 409 71.02 −2.60 1.562 −2.373 0.067 ——— 0.071 1454.5 266 TCCATCCCTGTGGAAGCACA 410 71.74 −1.70 1.669 −1.591 0.430 ——— 0.032 1676.8 267 CCATCCCTGTGGAAGCACAT 411 70.20 −2.20 1.443 −2.025 0.125 ——— 0.026 2268.9 268 CATCCCTGTGGAAGCACATT 412 67.07 −2.20 0.983 −2.025 −0.160 ——— 0.004 1682.6 269 ATCCCTGTGGAAGCACATTG 413 65.82 −2.20 0.801 −2.025 −0.273 ——— 0.070 1753.9 270 TCCCTGTGGAAGCACATTGT 414 68.98 −2.20 1.263 −2.025 0.014 ———−0.220 1281.8 271 CCCTGTGGAAGCACATTGTA 415 66.92 −2.20 0.962 −2.025 −0.173 ———−0.344 1227.8 272 CCTGTGGAAGCACATTGTAC 416 63.84 −2.20 0.509 −2.025 −0.454 ———−0.337 700.3 273 CTGTGGAAGCACATTGTACT 417 62.01 −2.20 0.241 −2.025 −0.620 ———−0.307 618.7 274 TGTGGAAGCACATTGTACTG 418 59.99 −2.00 −0.056 −1.851 −0.738 ———−0.324 771.5 275 GTGGAAGCACATTGTACTGA 419 61.39 −0.50 0.149 −0.547 −0.115 ———−0.347 1180.6 276 TGGAAGCACATTGTACTGAT 420 58.35 0.50 −0.296 0.323 −0.061 ———−0.331 1160.5 277 GGAAGCACATTGTACTGATA 421 57.86 0.50 −0.368 0.323 −0.106 ———−0.239 1314.7 278 GAAGCACATTGTACTGATAT 422 55.32 0.50 −0.740 0.323 −0.336 ———−0.141 1102.5 279 AAGCACATTGTACTGATATC 423 55.30 0.50 −0.744 0.323 −0.339 ———−0.209 1222.1 280 AGCACATTGTACTGATATCT 424 59.26 0.50 −0.162 0.323 0.022 ———−0.302 1893.2 281 GCACATTGTACTGATATCTA 425 58.48 0.50 −0.277 0.323 −0.049 ———−0.398 2097.7 282 CACATTGTACTGATATCTAA 426 52.51 0.50 −1.152 0.323 −0.592 ———−0.446 1237.8 283 ACATTGTACTGATATCTAAT 427 51.20 0.50 −1.345 0.323 −0.711 ———−0.443 959.5 284 CATTGTACTGATATCTAATC 428 51.89 0.10 −1.244 −0.025 −0.781 ———−0.472 1149.1 285 ATTGTACTGATATCTAATCC 429 54.53 −0.30 −0.856 −0.373 −0.672 ———−0.490 2351.3 286 TTGTACTGATATCTAATCCC 430 58.41 −0.30 −0.287 −0.373 −0.320 ———−0.436 4191.6 287 TGTACTGATATCTAATCCCT 431 59.99 −0.30 −0.055 −0.373 −0.176 ———−0.320 5565.8 288 GTACTGATATCTAATCCCTG 432 59.99 −0.30 −0.055 −0.373 −0.176 ———−0.202 9980.2 289 TACTGATATCTAATCCCTGG 433 59.52 −0.30 −0.124 −0.373 −0.218 ———−0.084 6318.9 290 ACTGATATCTAATCCCTGGT 434 63.07 −0.30 0.397 −0.373 0.104 ——— 0.023 7749.5 291 CTGATATCTAATCCCTGGTG 435 62.43 −0.30 0.303 −0.373 0.046 ——— 0.184 8165.3 292 TGATATCTAATCCCTGGTGT 436 63.60 −0.30 0.474 −0.373 0.152 ——— 0.365 9107.6 293 GATATCTAATCCCTGGTGTC 437 65.19 0.10 0.707 −0.025 0.429 ——— 0.566 13914.0 294 ATATCTAATCCCTGGTGTCT 438 65.82 1.50 0.800 1.192 0.949 ——— 0.698 15093.0 295 TATCTAATCCCTGGTGTCTC 439 67.41 1.50 1.033 1.192 1.093 ——— 0.822 18647.0 296 ATCTAATCCCTGGTGTCTCA 440 69.20 1.30 1.296 1.018 1.190  0.904 21810.0 297 TCTAATCCCTGGTGTCTCAT 441 69.20 0.80 1.296 0.583 1.025  0.996 20102.0 298 CTAATCCCTGGTGTCTCATT 442 67.98 0.80 1.117 0.583 0.914  1.052 20967.0 299 TAATCCCTGGTGTCTCATTG 443 65.90 0.80 0.811 0.583 0.725  1.092 18200.0 300 AATCCCTGGTGTCTCATTGT 444 69.78 0.80 1.380 0.583 1.077  1.088 19845.0 301 ATCCCTGGTGTCTCATTGTT 445 72.61 0.80 1.797 0.583 1.336  1.057 19231.0 302 TCCCTGGTGTCTCATTGTTT 446 73.04 0.80 1.860 0.583 1.375  0.981 17629.0 303 CCCTGGTGTCTCATTGTTTA 447 70.72 0.80 1.519 0.583 1.164  0.918 17009.0 304 CCTGGTGTCTCATTGTTTAT 448 66.82 0.80 0.946 0.583 0.808 ——— 0.800 11580.0 305 CTGGTGTCTCATTGTTTATA 449 62.17 0.80 0.264 0.583 0.386 ——— 0.600 8374.6 306 TGGTGTCTCATTGTTTATAC 450 60.65 0.90 0.042 0.670 0.281 ——— 0.355 6153.3 307 GGTGTCTCATTGTTTATACT 451 62.88 0.20 0.369 0.062 0.252 ——— 0.177 7134.0 308 GTGTCTCATTGTTTATACTA 452 59.43 0.20 −0.138 0.062 −0.062 ——— 0.050 4435.2 309 TGTCTCATTGTTTATACTAG 453 56.35 0.20 −0.589 0.062 −0.342 ———−0.043 2035.5 310 GTCTCATTGTTTATACTAGG 454 59.21 0.20 −0.170 0.062 −0.082 ———−0.149 2466.6 311 TCTCATTGTTTATACTAGGT 455 59.21 0.20 −0.170 0.062 −0.082 ———−0.268 1080.9 312 CTCATTGTTTATACTAGGTA 456 57.15 0.20 −0.472 0.062 −0.269 ———−0.325 956.0 313 TCATTGTTTATACTAGGTAT 457 55.08 0.20 −0.776 0.062 −0.458 ———−0.302 529.4 314 CATTGTTTATACTAGGTATG 458 53.70 0.20 −0.978 0.062 −0.583 ———−0.328 471.4 315 ATTGTTTATACTAGGTATGG 459 55.01 0.20 −0.785 0.062 −0.463 ———−0.389 510.4 316 TTGTTTATACTAGGTATGGT 460 58.17 0.20 −0.322 0.062 −0.176 ———−0.486 531.0 317 TGTTTATACTAGGTATGGTA 461 57.21 0.20 −0.463 0.062 −0.264 ———−0.560 613.3 318 GTTTATACTAGGTATGGTAA 462 55.23 0.00 −0.753 −0.112 −0.510 ———−0.620 685.1 319 TTTATACTAGGTATGGTAAA 463 50.42 0.00 −1.459 −0.112 −0.947 ———−0.639 300.0 320 TTATACTAGGTATGGTAAAT 464 50.12 0.00 −1.504 −0.112 −0.975 ———−0.672 316.1 321 TATACTAGGTATGGTAAATG 465 49.79 0.00 −1.551 −0.112 −1.004 ———−0.655 387.5 322 ATACTAGGTATGGTAAATGC 466 54.30 0.00 −0.889 −0.112 −0.594 ———−0.557 685.7 323 TACTAGGTATGGTAAATGCA 467 55.59 0.20 −0.700 0.062 −0.411 ———−0.430 759.6 324 ACTAGGTATGGTAAATGCAG 468 56.32 0.80 −0.593 0.583 −0.146 ———−0.291 1050.2 325 CTAGGTATGGTAAATGCAGT 469 58.78 1.10 −0.232 0.844 0.177 ———−0.157 1020.4 326 TAGGTATGGTAAATGCAGTA 470 56.24 1.10 −0.605 0.844 −0.054 ———−0.109 742.6 327 AGGTATGGTAAATGCAGTAT 471 56.81 1.10 −0.521 0.844 −0.002 ———−0.132 889.6 328 GGTATGGTAAATGCAGTATA 472 56.07 1.10 −0.631 0.844 −0.070 ———−0.182 858.8 329 GTATGGTAAATGCAGTATAC 473 54.02 1.10 −0.931 0.844 −0.256 ———−0.262 379.0 330 TATGGTAAATGCAGTATACT 474 53.06 0.40 −1.071 0.236 −0.575 ———−0.257 166.7 331 ATGGTAAATGCAGTATACTT 475 53.94 0.40 −0.943 0.236 −0.495 ———−0.249 215.3 332 TGGTAAATGCAGTATACTTC 476 55.21 0.40 −0.757 0.236 −0.380 ———−0.303 103.2 333 GGTAAATGCAGTATACTTCC 477 59.15 0.40 −0.178 0.236 −0.021 ———−0.326 246.3 334 GTAAATGCAGTATACTTCCT 478 58.53 0.80 −0.269 0.583 0.055 ———−0.303 163.4 335 TAAATGCAGTATACTTCCTG 479 55.54 0.10 −0.708 −0.025 −0.448 ———−0.264 294.1 336 AAATGCAGTATACTTCCTGA 480 57.36 −0.30 −0.441 −0.373 −0.415 ———−0.229 531.4 337 AATGCAGTATACTTCCTGAA 481 57.36 −0.30 −0.441 −0.373 −0.415 ———−0.233 1995.5 338 ATGCAGTATACTTCCTGAAG 482 59.50 −0.30 −0.128 −0.373 −0.221 ———−0.279 510.1 339 TGCAGTATACTTCCTGAAGT 483 62.63 −0.90 0.332 −0.895 −0.134 ———−0.264 555.4 340 GCAGTATACTTCCTGAAGTC 484 64.24 −1.10 0.568 −1.069 −0.054 ———−0.238 1214.0 341 CAGTATACTTCCTGAAGTCT 485 61.94 −1.10 0.230 −1.069 −0.263 ———−0.237 825.7 342 AGTATACTTCCTGAAGTCTT 486 61.00 −1.10 0.094 −1.069 −0.348 ———−0.261 1582.6 343 GTATACTTCCTGAAGTCTTC 487 62.28 −1.10 0.281 −1.069 −0.232 ———−0.278 2391.8 344 TATACTTCCTGAAGTCTTCA 488 60.34 −1.10 −0.004 −1.069 −0.409 ———−0.273 2276.3 345 ATACTTCCTGAAGTCTTCAT 489 60.91 −1.20 0.080 −1.156 −0.389 ———−0.252 2702.8 346 TACTTCCTGAAGTCTTCATC 490 62.40 −1.20 0.299 −1.156 −0.254 ———−0.274 3781.7 347 ACTTCCTGAAGTCTTCATCT 491 65.05 −1.20 0.686 −1.156 −0.014 ———−0.314 5343.4 348 CTTCCTGAAGTCTTCATCTA 492 63.86 −1.20 0.512 −1.156 −0.122 ———−0.314 6309.0 349 TTCCTGAAGTCTTCATCTAA 493 59.70 −1.20 −0.098 −1.156 −0.500 ———−0.332 6372.4 350 TCCTGAAGTCTTCATCTAAG 494 59.55 −1.20 −0.120 −1.156 −0.513 ———−0.369 3835.3 351 CCTGAAGTCTTCATCTAAGG 495 60.76 −1.20 0.057 −1.156 −0.404 ———−0.423 8925.5 352 CTGAAGTCTTCATCTAAGGG 496 59.48 −1.20 −0.130 −1.156 −0.520 ———−0.472 1211.8 353 TGAAGTCTTCATCTAAGGGA 497 58.84 −1.00 −0.224 −0.982 −0.512 ———−0.414 609.4 354 GAAGTCTTCATCTAAGGGAA 498 56.91 −0.10 −0.507 −0.199 −0.390 ———−0.358 629.1 355 AAGTCTTCATCTAAGGGAAC 499 56.13 −0.10 −0.622 −0.199 −0.461 ———−0.341 749.3 356 AGTCTTCATCTAAGGGAACT 500 60.12 −0.10 −0.036 −0.199 −0.098 ———−0.371 805.6 357 GTCTTCATCTAAGGGAACTG 501 59.84 −0.10 −0.077 −0.199 −0.124 ———−0.449 817.0 358 TCTTCATCTAAGGGAACTGA 502 58.11 −0.10 −0.331 −0.199 −0.281 ———−0.536 327.1 359 CTTCATCTAAGGGAACTGAA 503 54.95 −0.60 −0.794 −0.634 −0.733 ———−0.645 320.0 360 TTCATCTAAGGGAACTGAAA 504 51.39 −0.60 −1.316 −0.634 −1.057 −0.822 84.1 361 TCATCTAAGGGAACTGAAAA 505 49.50 0.10 −1.595 −0.025 −0.998 −1.002 67.7 362 CATCTAAGGGAACTGAAAAA 506 46.98 0.10 −1.963 −0.025 −1.227 −1.171 62.2 363 ATCTAAGGGAACTGAAAAAT 507 45.78 0.10 −2.140 −0.025 −1.336 −1.298 78.9 364 TCTAAGGGAACTGAAAAATA 508 45.27 0.10 −2.214 −0.025 −1.382 −1.328 43.2 365 CTAAGGGAACTGAAAAATAT 509 44.36 0.10 −2.349 −0.025 −1.466 −1.322 50.4 366 TAAGGGAACTGAAAAATATG 510 42.71 0.10 −2.591 −0.025 −1.616 −1.242 43.7 367 AAGGGAACTGAAAAATATGC 511 46.54 0.10 −2.028 −0.025 −1.267 −1.163 45.6 368 AGGGAACTGAAAAATATGCA 512 49.21 0.30 −1.637 0.149 −0.958 −1.119 49.8 369 GGGAACTGAAAAATATGCAT 513 49.11 1.20 −1.651 0.931 −0.670 −1.082 53.2 370 GGAACTGAAAAATATGCATC 514 47.87 1.20 −1.834 0.931 −0.783 −0.958 56.6 371 GAACTGAAAAATATGCATCA 515 46.82 0.60 −1.987 0.410 −1.076 −0.844 45.3 372 AACTGAAAAATATGCATCAC 516 46.12 0.40 −2.090 0.236 −1.206 −0.773 56.3 373 ACTGAAAAATATGCATCACC 517 51.18 0.40 −1.347 0.236 −0.746 ———−0.702 61.7 374 CTGAAAAATATGCATCACCC 518 54.20 0.40 −0.905 0.236 −0.471 ———−0.616 224.5 375 TGAAAAATATGCATCACCCA 519 53.65 0.60 −0.985 0.410 −0.455 ———−0.476 413.0 376 GAAAAATATGCATCACCCAC 520 54.14 1.30 −0.913 1.018 −0.179 ———−0.289 1584.0 377 AAAAATATGCATCACCCACA 521 54.14 1.30 −0.913 1.018 −0.179 ———−0.097 1846.7 378 AAAATATGCATCACCCACAT 522 55.78 1.10 −0.673 0.844 −0.096 ——— 0.096 2445.8 379 AAATATGCATCACCCACATC 523 58.72 0.90 −0.241 0.670 0.105 ——— 0.291 3709.4 380 AATATGCATCACCCACATCC 524 64.13 0.90 0.552 0.670 0.597 ——— 0.494 4548.4 381 ATATGCATCACCCACATCCA 525 67.27 0.90 1.013 0.670 0.883 ——— 0.680 5254.1 382 TATGCATCACCCACATCCAG 526 67.53 0.90 1.051 0.670 0.906  0.864 5527.2 383 ATGCATCACCCACATCCAGT 527 71.21 0.90 1.590 0.670 1.241  0.991 6916.9 384 TGCATCACCCACATCCAGTA 528 70.68 0.70 1.513 0.496 1.127  1.030 5861.4 385 GCATCACCCACATCCAGTAC 529 71.39 0.70 1.617 0.496 1.191  1.043 8078.4 386 CATCACCCACATCCAGTACT 530 69.16 0.70 1.290 0.496 0.988  1.013 4148.8 387 ATCACCCACATCCAGTACTG 531 67.91 0.70 1.107 0.496 0.875  0.913 3317.1 388 TCACCCACATCCAGTACTGT 532 71.15 0.10 1.582 −0.025 0.971 ——— 0.830 2486.4 389 CACCCACATCCAGTACTGTT 533 69.94 −0.40 1.404 −0.460 0.696 ——— 0.714 2746.4 390 ACCCACATCCAGTACTGTTA 534 68.25 −0.40 1.157 −0.460 0.543 ——— 0.506 2133.0 391 CCCACATCCAGTACTGTTAC 535 68.25 −0.40 1.157 −0.460 0.543 ——— 0.297 2197.0 392 CCACATCCAGTACTGTTACT 536 66.50 −0.40 0.900 −0.460 0.383 ——— 0.066 1824.0 393 CACATCCAGTACTGTTACTG 537 62.61 −1.90 0.329 −1.764 −0.467 ———−0.137 1675.2 394 ACATCCAGTACTGTTACTGA 538 62.71 −2.30 0.344 −2.112 −0.590 ———−0.313 1219.8 395 CATCCAGTACTGTTACTGAT 539 62.12 −2.30 0.258 −2.112 −0.643 ———−0.504 1414.0 396 ATCCAGTACTGTTACTGATT 540 61.21 −2.30 0.124 −2.112 −0.726 ———−0.700 1710.7 397 TCCAGTACTGTTACTGATTT 541 61.58 −2.30 0.178 −2.112 −0.692 ———−0.713 2280.7 398 CCAGTACTGTTACTGATTTT 542 60.48 −2.30 0.017 −2.112 −0.792 ———−0.659 2847.7 399 CAGTACTGTTACTGATTTTT 543 56.84 −1.90 −0.518 −1.764 −0.992 ———−0.635 2830.2 400 AGTACTGTTACTGATTTTTT 544 55.82 −0.30 −0.666 −0.373 −0.555 ———−0.588 4336.3 401 GTACTGTTACTGATTTTTTC 545 57.04 0.40 −0.488 0.236 −0.213 ———−0.548 6581.1 402 TACTGTTACTGATTTTTTCT 546 55.95 −0.10 −0.649 −0.199 −0.478 ———−0.516 5406.6 403 ACTGTTACTGATTTTTTCTT 547 56.89 −0.10 −0.510 −0.199 −0.392 ———−0.450 6083.1 404 CTGTTACTGATTTTTTCTTT 548 56.67 −0.10 −0.542 −0.199 −0.412 ———−0.482 6585.7 405 TGTTACTGATTTTTTCTTTT 549 54.96 −0.10 −0.793 −0.199 −0.567 ———−0.575 3923.2 406 GTTACTGATTTTTTCTTTTT 550 55.36 −0.10 −0.734 −0.199 −0.531 ———−0.646 4093.5 407 TTACTGATTTTTTCTTTTTT 551 52.62 −0.10 −1.136 −0.199 −0.780 ———−0.730 1381.5 408 TACTGATTTTTTCTTTTTTA 552 51.70 −0.10 −1.272 −0.199 −0.864 −0.784 1194.3 409 ACTGATTTTTTCTTTTTTAA 553 50.45 −0.10 −1.454 −0.199 −0.977 −0.746 2371.3 410 CTGATTTTTTCTTTTTTAAC 554 50.45 −0.10 −1.454 −0.199 −0.977 ———−0.682 395.9 411 TGATTTTTTCTTTTTTAACC 555 52.50 −0.10 −1.155 −0.199 −0.792 ———−0.583 230.7 412 GATTTTTTCTTTTTTAACCC 556 56.43 0.30 −0.578 0.149 −0.302 ———−0.423 314.9 413 ATTTTTTCTTTTTTAACCCT 557 57.05 0.80 −0.487 0.583 −0.080 ———−0.246 276.1 414 TTTTTTCTTTTTTAACCCTG 558 56.99 0.80 −0.495 0.583 −0.085 ———−0.046 273.3 415 TTTTTCTTTTTTAACCCTGC 559 60.68 0.80 0.045 0.583 0.250 ——— 0.093 628.4 416 TTTTCTTTTTTAACCCTGCG 560 60.85 0.80 0.071 0.583 0.265 ——— 0.155 4661.4 417 TTTCTTTTTTAACCCTGCGG 561 62.93 0.70 0.377 0.496 0.422 ——— 0.167 411.2 418 TTCTTTTTTAACCCTGCGGG 562 65.01 −0.60 0.681 −0.634 0.181 ——— 0.156 289.5 419 TCTTTTTTAACCCTGCGGGA 563 65.91 −1.00 0.813 −0.982 0.131 ——— 0.130 244.8 420 CTTTTTTAACCCTGCGGGAT 564 64.52 −1.00 0.610 −0.982 0.005 ——— 0.096 250.7 421 TTTTTTAACCCTGCGGGATG 565 62.66 −1.00 0.337 −0.982 −0.164 ——— 0.067 207.8 422 TTTTTAACCCTGCGGGATGT 566 65.23 −1.00 0.713 −0.982 0.069 ——— 0.106 255.8 423 TTTTAACCCTGCGGGATGTG 567 64.80 −1.00 0.651 −0.982 0.030 ——— 0.142 356.8 424 TTTAACCCTGCGGGATGTGG 568 66.83 −1.00 0.949 −0.982 0.215 ——— 0.201 497.8 425 TTAACCCTGCGGGATGTGGT 569 69.50 −1.00 1.339 −0.982 0.457 ——— 0.318 754.3 426 TAACCCTGCGGGATGTGGTA 570 68.63 −1.00 1.212 −0.982 0.378 ——— 0.434 902.4 427 AACCCTGCGGGATGTGGTAT 571 69.14 −1.00 1.286 −0.982 0.424 ——— 0.555 1186.6 428 ACCCTGCGGGATGTGGTATT 572 71.66 −1.00 1.657 −0.982 0.654 ——— 0.595 1514.9 429 CCCTGCGGGATGTGGTATTC 573 72.66 −0.60 1.804 −0.634 0.878 ——— 0.569 2407.6 430 CCTGCGGGATGTGGTATTCC 574 72.66 −0.60 1.804 −0.634 0.878 ——— 0.526 3019.4 431 CTGCGGGATGTGGTATTCCT 575 71.02 −1.30 1.563 −1.243 0.497 ——— 0.426 3275.3 432 TGCGGGATGTGGTATTCCTA 576 68.54 −1.30 1.199 −1.243 0.271 ——— 0.291 2830.8 433 GCGGGATGTGGTATTCCTAA 577 66.48 −1.30 0.896 −1.243 0.083 ——— 0.108 2620.5 434 CGGGATGTGGTATTCCTAAT 578 62.46 −1.30 0.307 −1.243 −0.282 ———−0.058 1827.8 435 GGGATGTGGTATTCCTAATT 579 62.37 −1.30 0.294 −1.243 −0.290 ———−0.211 1957.4 436 GGATGTGGTATTCCTAATTG 580 59.71 −0.90 −0.097 −0.895 −0.400 ———−0.330 1686.2 437 GATGTGGTATTCCTAATTGA 581 58.45 −0.20 −0.281 −0.286 −0.283 ———−0.396 1395.0 438 ATGTGGTATTCCTAATTGAA 582 55.24 −0.20 −0.752 −0.286 −0.575 ———−0.444 1245.7 439 TGTGGTATTCCTAATTGAAC 583 55.76 −0.30 −0.675 −0.373 −0.561 ———−0.473 1314.0 440 GTGGTATTCCTAATTGAACT 584 57.73 −0.30 −0.387 −0.373 −0.382 ———−0.470 1818.7 441 TGGTATTCCTAATTGAACTT 585 55.15 −0.30 −0.765 −0.373 −0.616 ———−0.474 880.3 442 GGTATTCCTAATTGAACTTC 586 56.47 −0.30 −0.572 −0.373 −0.496 ———−0.413 1419.0 443 GTATTCCTAATTGAACTTCC 587 57.76 −0.30 −0.383 −0.373 −0.379 ———−0.343 1567.9 444 TATTCCTAATTGAACTTCCC 588 58.57 −0.30 −0.264 −0.373 −0.306 ———−0.248 1959.4 445 ATTCCTAATTGAACTTCCCA 589 60.26 −0.30 −0.016 −0.373 −0.152 ———−0.161 2971.8 446 TTCCTAATTGAACTTCCCAG 590 60.45 −0.10 0.013 −0.199 −0.068 ———−0.200 1898.5 447 TCCTAATTGAACTTCCCAGA 591 61.36 0.70 0.146 0.496 0.279 ———−0.300 1392.3 448 CCTAATTGAACTTCCCAGAA 592 58.27 0.70 −0.308 0.496 −0.002 ———−0.397 1143.2 449 CTAATTGAACTTCCCAGAAG 593 54.92 −0.70 −0.800 −0.721 −0.770 ———−0.467 427.7 450 TAATTGAACTTCCCAGAAGT 594 55.84 −1.90 −0.664 −1.764 −1.082 ———−0.545 148.5 451 AATTGAACTTCCCAGAAGTC 595 57.61 −2.10 −0.404 −1.938 −0.987 ———−0.677 259.1 452 ATTGAACTTCCCAGAAGTCT 596 61.42 −2.10 0.154 −1.938 −0.641 −0.751 241.9 453 TTGAACTTCCCAGAAGTCTT 597 61.76 −2.10 0.205 −1.938 −0.609 −0.730 808.1 454 TGAACTTCCCAGAAGTCTTG 598 61.34 −2.10 0.143 −1.938 −0.648 ———−0.586 351.6 455 GAACTTCCCAGAAGTCTTGA 599 62.71 −2.10 0.344 −1.938 −0.523 ———−0.415 499.7 456 AACTTCCCAGAAGTCTTGAG 600 61.63 −2.10 0.186 −1.938 −0.621 ———−0.262 407.4 457 ACTTCCCAGAAGTCTTGAGT 601 66.97 −1.90 0.969 −1.764 −0.069 ———−0.138 492.1 458 CTTCCCAGAAGTCTTGAGTT 602 66.75 −1.00 0.937 −0.982 0.208 ———−0.019 736.1 459 TTCCCAGAAGTCTTGAGTTC 603 66.31 −0.20 0.872 −0.286 0.432 ——— 0.058 815.2 460 TCCCAGAAGTCTTGAGTTCT 604 67.98 −1.20 1.116 −1.156 0.253 ——— 0.101 888.8 461 CCCAGAAGTCTTGAGTTCTC 605 67.98 −1.40 1.116 −1.330 0.187 ——— 0.049 2021.6 462 CCAGAAGTCTTGAGTTCTCT 606 66.10 −1.40 0.842 −1.330 0.017 ———−0.013 1988.5 463 CAGAAGTCTTGAGTTCTCTT 607 62.41 −1.40 0.300 −1.330 −0.319 ———−0.082 2008.8 464 AGAAGTCTTGAGTTCTCTTA 608 60.43 −1.20 0.009 −1.156 −0.434 ———−0.105 2631.8 465 GAAGTCTTGAGTTCTCTTAT 609 60.20 −0.50 −0.025 −0.547 −0.223 ———−0.151 3052.8 466 AAGTCTTGAGTTCTCTTATT 610 59.12 0.30 −0.183 0.149 −0.057 ———−0.212 3509.3 467 AGTCTTGAGTTCTCTTATTA 611 60.75 0.30 0.056 0.149 0.091 ———−0.211 3221.6 468 GTCTTGAGTTCTCTTATTAA 612 58.29 0.30 −0.305 0.149 −0.132 ———−0.216 3677.1 469 TCTTGAGTTCTCTTATTAAG 613 55.25 0.30 −0.751 0.149 −0.409 ———−0.238 1176.6 470 CTTGAGTTCTCTTATTAAGT 614 57.04 0.10 −0.488 −0.025 −0.312 ———−0.255 1168.1 471 TTGAGTTCTCTTATTAAGTT 615 55.29 0.10 −0.745 −0.025 −0.471 ———−0.292 666.3 472 TGAGTTCTCTTATTAAGTTC 616 56.35 0.10 −0.589 −0.025 −0.375 ———−0.271 674.0 473 GAGTTCTCTTATTAAGTTCT 617 58.57 0.10 −0.263 −0.025 −0.173 ———−0.256 1471.4 474 AGTTCTCTTATTAAGTTCTC 618 58.61 0.10 −0.257 −0.025 −0.169 ———−0.240 1493.5 475 GTTCTCTTATTAAGTTCTCT 619 60.59 0.10 0.032 −0.025 0.011 ———−0.247 2191.5 476 TTCTCTTATTAAGTTCTCTG 620 57.16 0.10 −0.471 −0.025 −0.301 ———−0.317 1410.3 477 TCTCTTATTAAGTTCTCTGA 621 58.23 0.10 −0.314 −0.025 −0.204 ———−0.413 1262.8 478 CTCTTATTAAGTTCTCTGAA 622 54.79 0.10 −0.817 −0.025 −0.516 ———−0.519 1072.9 479 TCTTATTAAGTTCTCTGAAA 623 50.95 0.10 −1.382 −0.025 −0.866 ———−0.629 540.9 480 CTTATTAAGTTCTCTGAAAT 624 49.77 0.50 −1.554 0.323 −0.841 ———−0.695 539.2 481 TTATTAAGTTCTCTGAAATC 625 48.99 0.50 −1.668 0.323 −0.912 −0.768 709.0 482 TATTAAGTTCTCTGAAATCT 626 50.64 0.50 −1.427 0.323 −0.762 −0.775 978.1 483 ATTAAGTTCTCTGAAATCTA 627 50.64 0.50 −1.427 0.323 −0.762 −0.732 1217.7 484 TTAAGTTCTCTGAAATCTAC 628 51.15 0.50 −1.352 0.323 −0.716 ———−0.693 1748.1 485 TAAGTTCTCTGAAATCTACT 629 52.79 0.50 −1.112 0.323 −0.567 ———−0.646 2511.5 486 AAGTTCTCTGAAATCTACTA 630 52.79 0.50 −1.112 0.323 −0.567 ———−0.643 2997.2 487 AGTTCTCTGAAATCTACTAA 631 52.79 0.50 −1.112 0.323 −0.567 ———−0.663 2887.6 488 GTTCTCTGAAATCTACTAAT 632 52.65 0.50 −1.133 0.323 −0.580 ———−0.725 4421.3 489 TTCTCTGAAATCTACTAATT 633 50.14 0.70 −1.500 0.496 −0.741 −0.832 1937.7 490 TCTCTGAAATCTACTAATTT 634 50.14 0.20 −1.500 0.062 −0.906 −0.962 1773.3 491 CTCTGAAATCTACTAATTTT 635 49.31 −0.30 −1.622 −0.373 −1.147 −1.102 1491.1 492 TCTGAAATCTACTAATTTTC 636 48.55 −0.60 −1.734 −0.634 −1.316 −1.171 376.6 493 CTGAAATCTACTAATTTTCT 637 49.31 −1.30 −1.622 −1.243 −1.478 −1.178 371.9 494 TGAAATCTACTAATTTTCTC 638 48.55 −1.30 −1.734 −1.243 −1.547 −1.092 415.2 495 GAAATCTACTAATTTTCTCC 639 52.45 −0.90 −1.161 −0.895 −1.060 −0.938 1097.9 496 AAATCTACTAATTTTCTCCA 640 52.47 −0.10 −1.158 −0.199 −0.794 −0.778 1429.1 497 AATCTACTAATTTTCTCCAT 641 54.25 0.90 −0.897 0.670 −0.301 ———−0.620 1812.5 495 ATCTACTAATTTTCTCCATT 642 56.46 1.00 −0.572 0.757 −0.067 ———−0.485 1943.4 499 TCTACTAATTTTCTCCATTT 643 56.80 0.50 −0.523 0.323 −0.202 ———−0.421 1506.1 500 CTACTAATTTTCTCCATTTA 644 54.93 0.50 −0.797 0.323 −0.372 ———−0.376 1694.7 501 TACTAATTTTCTCCATTTAG 645 53.14 0.30 −1.060 0.149 −0.600 ———−0.396 946.7 502 ACTAATTTTCTCCATTTAGT 646 56.69 −0.70 −0.539 −0.721 −0.605 ———−0.407 1114.3 503 CTAATTTTCTCCATTTAGTA 647 55.57 0.00 −0.704 −0.112 −0.479 ———−0.369 963.9 504 TAATTTTCTCCATTTAGTAC 648 54.12 0.50 −0.917 0.323 −0.446 ———−0.274 1347.9 505 AATTTTCTCCATTTAGTACT 649 56.69 0.70 −0.539 0.496 −0.145 ———−0.130 2067.7 506 ATTTTCTCCATTTAGTACTG 650 58.66 0.80 −0.250 0.583 0.067 ——— 0.037 2724.2 507 TTTTCTCCATTTAGTACTGT 651 61.92 0.60 0.228 0.410 0.297 ——— 0.186 3367.9 508 TTTCTCCATTTAGTACTGTC 652 63.10 0.60 0.401 0.410 0.404 ——— 0.314 5235.8 509 TTCTCCATTTAGTACTGTCT 653 64.84 0.60 0.656 0.410 0.562 ——— 0.377 6423.5 510 TCTCCATTTAGTACTGTCTT 654 64.84 0.60 0.656 0.410 0.562 ——— 0.396 7758.9 511 CTCCATTTAGTACTGTCTTT 655 63.63 0.60 0.479 0.410 0.453 ——— 0.342 8001.5 512 TCCATTTAGTACTGTCTTTT 656 61.92 0.60 0.228 0.410 0.297 ——— 0.273 5512.4 513 CCATTTAGTACTGTCTTTTT 657 60.78 0.60 0.061 0.410 0.194 ——— 0.210 5300.0 514 CATTTAGTACTGTCTTTTTT 658 57.04 0.80 −0.489 0.583 −0.081 ——— 0.147 3902.1 515 ATTTAGTACTGTCTTTTTTC 659 57.08 0.80 −0.482 0.583 −0.077 ——— 0.099 4641.8 516 TTTAGTACTGTCTTTTTTCT 660 59.26 0.80 −0.162 0.583 0.121 ——— 0.084 4888.4 517 TTAGTACTGTCTTTTTTCTT 661 59.26 0.80 −0.162 0.583 0.121 ——— 0.160 5477.3 518 TAGTACTGTCTTTTTTCTTT 662 59.26 0.80 −0.162 0.583 0.121 ——— 0.242 5064.9 519 AGTACTGTCTTTTTTCTTTA 663 59.26 1.00 −0.162 0.757 0.187 ——— 0.310 5580.3 520 GTACTGTCTTTTTTCTTTAT 664 59.04 2.70 −0.195 2.236 0.729 ——— 0.400 5478.3 521 TACTGTCTTTTTTCTTTATG 665 55.71 2.90 −0.683 2.410 0.492 ——— 0.480 2275.5 522 ACTGTCTTTTTTCTTTATGG 666 59.07 1.70 −0.190 1.366 0.402 ——— 0.524 1730.8 523 CTGTCTTTTTTCTTTATGGC 667 62.92 1.70 0.374 1.366 0.751 ——— 0.449 2405.5 524 TGTCTTTTTTCTTTATGGCA 668 62.14 1.70 0.260 1.366 0.680 ——— 0.258 1942.0 525 GTCTTTTTTCTTTATGGCAA 669 60.05 1.50 −0.047 1.192 0.424 ——— 0.068 2085.6 526 TCTTTTTTCTTTATGGCAAA 670 54.99 0.60 −0.788 0.410 −0.333 ———−0.106 493.2 527 CTTTTTTCTTTATGGCAAAT 671 53.75 0.10 −0.971 −0.025 −0.612 ———−0.309 532.7 528 TTTTTTCTTTATGGCAAATA 672 51.30 0.10 −1.331 −0.025 −0.835 ———−0.507 280.0 529 TTTTTCTTTATGGCAAATAC 673 51.49 0.10 −1.302 −0.025 −0.817 ———−0.640 440.8 530 TTTTCTTTATGGCAAATACT 674 53.08 0.10 −1.069 −0.025 −0.672 ———−0.652 463.1 531 TTTCTTTATGGCAAATACTG 675 52.74 0.10 −1.119 −0.025 −0.704 ———−0.639 579.0 532 TTCTTTATGGCAAATACTGG 676 54.90 0.10 −0.802 −0.025 −0.507 ———−0.572 673.7 533 TCTTTATGGCAAATACTGGA 677 55.85 0.10 −0.663 −0.025 −0.421 ———−0.504 837.0 534 CTTTATGGCAAATACTGGAG 678 54.78 0.10 −0.820 −0.025 −0.518 ———−0.490 1061.9 535 TTTATGGCAAATACTGGAGT 679 55.74 0.30 −0.679 0.149 −0.365 ———−0.507 855.0 536 TTATGGCAAATACTGGAGTA 680 54.87 0.60 −0.806 0.410 −0.344 ———−0.562 775.0 537 TATGGCAAATACTGGAGTAT 681 54.56 0.00 −0.852 −0.112 −0.571 ———−0.591 773.6 538 ATGGCAAATACTGGAGTATT 682 55.42 −1.00 −0.726 −0.982 −0.823 ———−0.647 702.5 539 TGGCAAATACTGGAGTATTG 683 55.37 −1.20 −0.733 −1.156 −0.893 −0.775 387.5 540 GGCAAATACTGGAGTATTGT 684 58.33 −1.20 −0.298 −1.156 −0.624 −0.924 435.3 541 GCAAATACTGGAGTATTGTA 685 55.24 −1.20 −0.753 −1.156 −0.906 −0.974 93.7 542 CAAATACTGGAGTATTGTAT 686 51.30 −1.20 −1.331 −1.156 −1.264 −0.913 50.0 543 AAATACTGGAGTATTGTATG 687 49.96 −1.20 −1.527 −1.156 −1.386 −0.809 50.4 544 AATACTGGAGTATTGTATGG 688 54.30 −1.00 −0.890 −0.982 −0.925 ———−0.688 64.7 545 ATACTGGAGTATTGTATGGA 689 57.60 −0.30 −0.406 −0.373 −0.394 ———−0.483 76.0 546 TACTGGAGTATTGTATGGAT 690 57.60 0.40 −0.406 0.236 −0.162 ———−0.236 86.0 547 ACTGGAGTATTGTATGGATT 691 58.53 1.30 −0.269 1.018 0.220 ———−0.009 123.4 548 CTGGAGTATTGTATGGATTC 692 59.39 2.00 −0.144 1.627 0.529 ——— 0.135 121.5 549 TGGAGTATTGTATGGATTCT 693 59.39 1.80 −0.144 1.453 0.463 ——— 0.210 641.3 550 GGAGTATTGTATGGATTCTC 694 60.95 0.60 0.086 0.410 0.209 ——— 0.286 161.5 551 GAGTATTGTATGGATTCTCA 695 59.52 0.60 −0.124 0.410 0.079 ——— 0.321 129.9 552 AGTATTGTATGGATTCTCAG 696 58.31 1.10 −0.302 0.844 0.134 ——— 0.371 88.7 553 GTATTGTATGGATTCTCAGG 697 60.87 1.10 0.074 0.844 0.367 ——— 0.462 112.5 554 TATTGTATGGATTCTCAGGC 698 61.97 1.10 0.236 0.844 0.467 ——— 0.575 134.6 555 ATTGTATGGATTCTCAGGCC 699 66.52 1.10 0.902 0.844 0.880 ——— 0.669 191.6 556 TTGTATGGATTCTCAGGCCC 700 70.34 0.70 1.463 0.496 1.096 ——— 0.714 254.5 557 TGTATGGATTCTCAGGCCCA 701 71.11 0.20 1.577 0.062 1.001 ——— 0.738 332.2 558 GTATGGATTCTCAGGCCCAA 702 68.95 0.00 1.259 −0.112 0.738 ——— 0.761 415.6 559 TATGGATTCTCAGGCCCAAT 703 65.78 0.00 0.795 −0.112 0.450 ——— 0.774 285.0 560 ATGGATTCTCAGGCCCAATT 704 66.68 0.00 0.925 −0.112 0.531 ——— 0.737 464.0 561 TGGATTCTCAGGCCCAATTT 705 67.04 0.20 0.979 0.062 0.630 ——— 0.663 492.5 562 GGATTCTCAGGCCCAATTTT 706 67.51 1.10 1.048 0.844 0.970 ——— 0.624 639.7 563 GATTCTCAGGCCCAATTTTT 707 65.34 1.30 0.729 1.018 0.839 ——— 0.595 512.4 564 ATTCTCAGGCCCAATTTTTG 708 63.94 0.60 0.524 0.410 0.481 ——— 0.513 393.4 565 TTCTCAGGCCCAATTTTTGA 709 65.24 0.20 0.716 0.062 0.467 ——— 0.394 334.3 566 TCTCAGGCCCAATTTTTGAA 710 62.85 0.20 0.364 0.062 0.249 ——— 0.181 308.2 567 CTCAGGCCCAATTTTTGAAA 711 59.62 0.20 −0.109 0.062 −0.044 ———−0.048 199.2 568 TCAGGCCCAATTTTTGAAAT 712 57.85 0.20 −0.369 0.062 −0.205 ———−0.223 164.3 569 CAGGCCCAATTTTTGAAATT 713 56.95 −0.50 −0.501 −0.547 −0.518 ———−0.412 125.6 570 AGGCCCAATTTTTGAAATTT 714 56.09 −1.00 −0.627 −0.982 −0.762 ———−0.571 102.6 571 GGCCCAATTTTTGAAATTTT 715 56.23 −1.00 −0.606 −0.982 −0.749 ———−0.688 91.6 572 GCCCAATTTTTGAAATTTTC 716 55.07 −1.00 −0.777 −0.982 −0.855 −0.806 76.2 573 CCCAATTTTTGAAATTTTCC 717 54.96 −1.00 −0.792 −0.982 −0.864 −0.881 78.8 574 CCAATTTTTGAAATTTTCCC 718 54.96 −1.00 −0.792 −0.982 −0.864 −0.841 84.8 575 CAATTTTTGAAATTTTCCCT 719 53.17 −1.00 −1.055 −0.982 −1.027 −0.755 162.0 576 AATTTTTGAAATTTTCCCTT 720 52.25 −0.80 −1.190 −0.808 −1.045 ———−0.634 539.5 577 ATTTTTGAAATTTTCCCTTC 721 55.17 0.10 −0.762 −0.025 −0.482 ———−0.511 1787.3 578 TTTTTGAAATTTTCCCTTCC 722 58.88 0.10 −0.219 −0.025 −0.145 ———−0.389 6354.2 579 TTTTGAAATTTTCCCTTCCT 723 60.39 0.10 0.004 −0.025 −0.007 ———−0.243 9513.6 580 TTTGAAATTTTCCCTTCCTT 724 60.39 0.10 0.004 −0.025 −0.007 ———−0.062 10660.0 581 TTGAAATTTTCCCTTCCTTT 725 60.39 0.10 0.004 −0.025 −0.007 ——— 0.107 11202.0 582 TGAAATTTTCCCTTCCTTTT 726 60.39 0.10 0.004 −0.025 −0.007 ——— 0.293 11543.0 583 GAAATTTTCCCTTCCTTTTC 727 61.81 0.40 0.212 0.236 0.221 ——— 0.596 14774.0 584 AAATTTTCCCTTCCTTTTCC 728 64.17 1.20 0.557 0.931 0.699  0.952 18197.0 585 AATTTTCCCTTCCTTTTCCA 729 67.39 1.70 1.030 1.366 1.158  1.307 21410.0 586 ATTTTCCCTTCCTTTTCCAT 730 69.58 4.00 1.351 3.366 2.117  1.679 22869.0 587 TTTTCCCTTCCTTTTCCATT 731 69.96 5.00 1.408 4.236 2.482  2.039 21818.0 588 TTTCCCTTCCTTTTCCATTT 732 69.96 5.00 1.408 4.236 2.482  2.113 21341.0 589 TTCCCTTCCTTTTCCATTTC 733 71.19 5.00 1.588 4.236 2.594  2.085 22063.0 590 TCCCTTCCTTTTCCATTTCT 734 72.77 5.00 1.820 4.236 2.738  1.863 22152.0 591 CCCTTCCTTTTCCATTTCTG 735 71.01 0.90 1.561 0.670 1.223  1.571 20764.0 592 CCTTCCTTTTCCATTTCTGT 736 70.68 0.20 1.513 0.062 0.961  1.289 12579.0 593 CTTCCTTTTCCATTTCTGTA 737 66.30 0.20 0.870 0.062 0.563  0.945 9036.3 594 TTCCTTTTCCATTTCTGTAC 738 64.87 0.20 0.660 0.062 0.433 ——— 0.505 8251.8 595 TCCTTTTCCATTTCTGTACA 739 65.74 0.20 0.788 0.062 0.512 ——— 0.257 20788.0 596 CCTTTTCCATTTCTGTACAA 740 62.11 0.20 0.256 0.062 0.182 ——— 0.024 7073.9 597 CTTTTCCATTTCTGTACAAA 741 56.39 0.20 −0.583 0.062 −0.338 ———−0.153 2932.4 598 TTTTCCATTTCTGTACAAAT 742 54.49 0.20 −0.862 0.062 −0.511 ———−0.300 1897.3 599 TTTCCATTTCTGTACAAATT 743 54.49 −0.30 −0.862 −0.373 −0.676 ———−0.449 2158.1 600 TTCCATTTCTGTACAAATTT 744 54.49 −0.30 −0.862 −0.373 −0.676 ———−0.608 2215.9 601 TCCATTTCTGTACAAATTTC 745 55.43 −0.30 −0.724 −0.373 −0.591 ———−0.695 2168.6 602 CCATTTCTGTACAAATTTCT 746 56.07 −0.30 −0.631 −0.373 −0.533 ———−0.708 2025.8 603 CATTTCTGTACAAATTTCTA 747 51.65 −0.30 −1.278 −0.373 −0.934 ———−0.708 1277.2 604 ATTTCTGTACAAATTTCTAC 748 50.83 −0.10 −1.398 −0.199 −0.943 −0.736 1944.8 605 TTTCTGTACAAATTTCTACT 749 52.78 0.40 −1.112 0.236 −0.600 −0.790 2504.3 606 TTCTGTACAAATTTCTACTA 750 51.90 0.40 −1.242 0.236 −0.681 −0.876 2941.5 607 TCTGTACAAATTTCTACTAA 751 49.84 0.40 −1.544 0.236 −0.868 −0.846 2694.8 608 CTGTACAAATTTCTACTAAT 752 48.73 0.40 −1.707 0.236 −0.969 −0.827 2610.7 609 TGTACAAATTTCTACTAATG 753 46.88 0.40 −1.979 0.236 −1.137 −0.845 1678.1 610 GTACAAATTTCTACTAATGC 754 50.66 0.60 −1.424 0.410 −0.727 −0.854 5877.3 611 TACAAATTTCTACTAATGCT 755 49.82 0.60 −1.547 0.410 −0.803 −0.849 4461.0 612 ACAAATTTCTACTAATGCTT 756 50.65 0.60 −1.425 0.410 −0.728 −0.816 5943.2 613 CAAATTTCTACTAATGCTTT 757 50.46 0.60 −1.453 0.410 −0.745 −0.753 6492.9 614 AAATTTCTACTAATGCTTTT 758 49.47 0.60 −1.599 0.410 −0.836 −0.745 6875.0 615 AATTTCTACTAATGCTTTTA 759 50.61 0.60 −1.431 0.410 −0.731 ———−0.727 7950.3 616 ATTTCTACTAATGCTTTTAT 760 52.40 0.20 −1.169 0.062 −0.701 ———−0.719 8314.8 617 TTTCTACTAATGCTTTTATT 761 52.72 0.20 −1.122 0.062 −0.672 ———−0.720 6885.8 618 TTCTACTAATGCTTTTATTT 762 52.72 0.20 −1.122 0.062 −0.672 ———−0.730 6443.2 619 TCTACTAATGCTTTTATTTT 763 52.72 0.20 −1.122 0.062 −0.672 −0.731 6331.0 620 CTACTAATGCTTTTATTTTT 764 51.81 0.20 −1.255 0.062 −0.755 ———−0.718 5952.5 621 TACTAATGCTTTTATTTTTT 765 50.18 0.20 −1.494 0.062 −0.903 ———−0.721 2662.8 622 ACTAATGCTTTTATTTTTTC 766 51.96 0.20 −1.233 0.062 −0.741 ———−0.667 3034.0 623 CTAATGCTTTTATTTTTTCT 767 53.41 0.20 −1.021 0.062 −0.609 ———−0.513 2198.5 624 TAATGCTTTTATTTTTTCTT 768 51.76 0.40 −1.263 0.236 −0.694 ———−0.315 1670.1 625 AATGCTTTTATTTTTTCTTC 769 53.61 1.10 −0.992 0.844 −0.294 ———−0.038 3039.4 626 ATGCTTTTATTTTTTCTTCT 770 57.66 2.10 −0.397 1.714 0.405 ——— 0.177 3873.8 627 TGCTTTTATTTTTTCTTCTG 771 57.60 2.80 −0.406 2.323 0.631 ——— 0.363 3609.7 628 GCTTTTATTTTTTCTTCTGT 772 60.96 3.10 0.087 2.583 1.036 ——— 0.464 4891.4 629 CTTTTATTTTTTCTTCTGTC 773 57.96 3.10 −0.353 2.583 0.763 ——— 0.480 3071.6 630 TTTTATTTTTTCTTCTGTCA 774 57.22 3.10 −0.461 2.583 0.696 ——— 0.391 2667.2 631 TTTATTTTTTCTTCTGTCAA 775 54.81 1.70 −0.816 1.366 0.013 ——— 0.312 2293.1 632 TTATTTTTTCTTCTGTCAAT 776 54.46 1.20 −0.866 0.931 −0.183 ——— 0.232 2123.0 633 TATTTTTTCTTCTGTCAATG 777 54.08 1.20 −0.922 0.931 −0.218 ——— 0.237 1914.7 634 ATTTTTTCTTCTGTCAATGG 778 57.36 1.20 −0.442 0.931 0.080 ——— 0.263 2174.1 635 TTTTTTCTTCTGTCAATGGC 779 61.67 1.20 0.192 0.931 0.473 ——— 0.372 3659.7 636 TTTTTCTTCTGTCAATGGCC 780 65.26 1.20 0.717 0.931 0.799 ——— 0.509 5217.7 637 TTTTCTTCTGTCAATGGCCA 781 66.11 1.20 0.843 0.931 0.877 ——— 0.569 4559.7 638 TTTCTTCTGTCAATGGCCAT 782 65.73 1.00 0.787 0.757 0.776 ——— 0.576 4347.7 639 TTCTTCTGTCAATGGCCATT 783 65.73 1.00 0.787 0.757 0.776 ——— 0.506 5267.4 640 TCTTCTGTCAATGGCCATTG 784 65.26 −0.60 0.718 −0.634 0.204 ——— 0.389 3922.8 641 CTTCTGTCAATGGCCATTGT 785 66.97 −1.30 0.968 −1.243 0.128 ——— 0.235 3608.6 642 TTCTGTCAATGGCCATTGTT 786 65.36 −1.30 0.733 −1.243 −0.018 ——— 0.044 1881.6 643 TCTGTCAATGGCCATTGTTT 787 65.36 −1.30 0.733 −1.243 −0.018 ———−0.139 1658.0 644 CTGTCAATGGCCATTGTTTA 788 63.32 −1.30 0.433 −1.243 −0.204 ———−0.255 1369.8 645 TGTCAATGGCCATTGTTTAA 789 59.38 −1.30 −0.144 −1.243 −0.562 ———−0.353 605.8 646 GTCAATGGCCATTGTTTAAC 790 59.99 −1.30 −0.055 −1.243 −0.506 ———−0.357 933.2 647 TCAATGGCCATTGTTTAACT 791 58.93 −1.30 −0.211 −1.243 −0.603 ———−0.331 441.8 648 CAATGGCCATTGTTTAACTT 792 57.97 −0.90 −0.352 −0.895 −0.558 ———−0.281 545.6 649 AATGGCCATTGTTTAACTTT 793 57.07 0.90 −0.483 0.670 −0.045 ———−0.173 781.4 650 ATGGCCATTGTTTAACTTTT 794 59.31 0.90 −0.156 0.670 0.158 ———−0.092 1027.3 651 TGGCCATTGTTTAACTTTTG 795 59.24 0.90 −0.165 0.670 0.152 ——— 0.021 1102.5 652 GGCCATTGTTTAACTTTTGG 796 61.84 0.30 0.216 0.149 0.190 ——— 0.156 935.7 653 GCCATTGTTTAACTTTTGGG 797 61.84 −0.10 0.216 −0.199 0.058 ——— 0.218 403.7 654 CCATTGTTTAACTTTTGGGC 798 61.84 0.30 0.216 0.149 0.190 ——— 0.251 269.3 655 CATTGTTTAACTTTTGGGCC 799 61.84 0.90 0.216 0.670 0.389 ——— 0.299 296.8 656 ATTGTTTAACTTTTGGGCCA 800 61.84 0.90 0.216 0.670 0.389 ——— 0.367 449.4 657 TTGTTTAACTTTTGGGCCAT 801 61.84 0.90 0.216 0.670 0.389 ——— 0.377 448.1 658 TGTTTAACTTTTGGGCCATC 802 62.91 0.90 0.373 0.670 0.486 ——— 0.340 584.9 659 GTTTAACTTTTGGGCCATCC 803 66.73 0.40 0.934 0.236 0.669 ——— 0.275 1032.4 660 TTTAACTTTTGGGCCATCCA 804 64.79 −0.70 0.649 −0.721 0.128 ——— 0.235 737.8 661 TTAACTTTTGGGCCATCCAT 805 64.44 −1.20 0.598 −1.156 −0.069 ——— 0.271 950.2 662 TAACTTTTGGGCCATCCATT 806 64.44 −1.20 0.598 −1.156 −0.069 ——— 0.310 1308.0 663 AACTTTTGGGCCATCCATTC 807 66.42 −1.20 0.888 −1.156 0.111 ——— 0.296 2360.1 664 ACTTTTGGGCCATCCATTCC 808 72.21 −1.20 1.738 −1.156 0.638 ——— 0.387 4946.0 665 CTTTTGGGCCATCCATTCCT 809 73.53 −1.20 1.930 −1.156 0.758 ——— 0.480 6789.2 666 TTTTGGGCCATCCATTCCTG 810 71.49 −1.20 1.632 −1.156 0.573 ——— 0.560 8150.6 667 TTTGGGCCATCCATTCCTGG 811 73.62 −1.20 1.945 −1.156 0.766 ——— 0.622 7589.0 668 TTGGGCCATCCATTCCTGGC 812 77.43 −2.80 2.504 −2.547 0.584 ——— 0.580 13914.0 669 TGGGCCATCCATTCCTGGCT 813 78.94 −3.50 2.725 −3.156 0.490 ——— 0.500 17513.0 670 GGGCCATCCATTCCTGGCTT 814 79.51 −3.50 2.809 −3.156 0.542 ——— 0.449 19883.0 671 GGCCATCCATTCCTGGCTTT 815 77.37 −3.50 2.494 −3.156 0.347 ——— 0.324 20103.0 672 GCCATCCATTCCTGGCTTTA 816 74.28 −3.10 2.040 −2.808 0.198 ——— 0.214 18622.9 673 CCATCCATTCCTGGCTTTAA 817 67.92 −1.30 1.109 −1.243 0.215 ——— 0.122 16915.0 674 CATCCATTCCTGGCTTTAAT 818 64.36 −1.30 0.585 −1.243 −0.109 ——— 0.028 13910.0 675 ATCCATTCCTGGCTTTAATT 819 63.53 −1.30 0.464 −1.243 −0.185 ———−0.009 12524.0 676 TCCATTCCTGGCTTTAATTT 820 63.88 −1.30 0.516 −1.243 −0.152 ———−0.005 11890.0 677 CCATTCCTGGCTTTAATTTT 821 62.81 −0.90 0.359 −0.895 −0.118 ——— 0.040 12839.0 678 CATTCCTGGCTTTAATTTTA 822 58.55 0.90 −0.266 0.670 0.090 ——— 0.126 9726.8 679 ATTCCTGGCTTTAATTTTAC 823 57.84 1.50 −0.371 1.192 0.223 ——— 0.238 8499.7 680 TTCCTGGCTTTAATTTTACT 824 59.78 1.90 −0.086 1.540 0.532 ——— 0.336 6800.4 681 TCCTGGCTTTAATTTTACTG 825 59.37 1.90 −0.146 1.540 0.494 ——— 0.396 5445.6 682 CCTGGCTTTAATTTTACTGG 826 60.53 1.90 0.024 1.540 0.600 ——— 0.434 2901.6 683 CTGGCTTTAATTTTACTGGT 827 59.77 1.90 −0.087 1.540 0.531 ——— 0.431 1174.2 684 TGGCTTTAATTTTACTGGTA 828 57.25 1.90 −0.458 1.540 0.301 ——— 0.268 521.3 685 GGCTTTAATTTTACTGGTAC 829 57.86 1.90 −0.368 1.540 0.357 ——— 0.066 611.1 686 GCTTTAATTTTACTGGTACA 830 56.55 1.80 −0.560 1.453 0.205 ———−0.148 287.6 687 CTTTAATTTTACTGGTACAG 831 52.66 0.40 −1.130 0.236 −0.611 ———−0.330 109.5 688 TTTAATTTTACTGGTACAGT 832 53.62 −0.80 −0.989 −0.808 −0.920 ———−0.454 59.5 689 TTAATTTTACTGGTACAGTC 833 54.59 −1.00 −0.847 −0.982 −0.898 ———−0.540 62.1 690 TAATTTTACTGGTACAGTCT 834 56.28 −1.00 −0.599 −0.982 −0.745 ———−0.632 59.4 691 AATTTTACTGGTACAGTCTC 835 58.27 −1.00 −0.308 −0.982 −0.564 ———−0.613 68.0 692 ATTTTACTGGTACAGTCTCA 836 61.78 −1.00 0.207 −0.982 −0.245 ———−0.561 72.9 693 TTTTACTGGTACAGTCTCAA 837 59.61 −1.00 −0.111 −0.982 −0.442 ———−0.515 62.2 694 TTTACTGGTACAGTCTCAAT 838 59.25 −1.00 −0.164 −0.982 −0.475 ———−0.439 64.5 695 TTACTGGTACAGTCTCAATA 839 58.30 −1.00 −0.303 −0.982 −0.561 ———−0.318 53.5 696 TACTGGTACAGTCTCAATAG 840 58.15 −1.00 −0.326 −0.982 −0.575 ———−0.166 57.8 697 ACTGGTACAGTCTCAATAGG 841 61.44 −0.80 0.157 −0.808 −0.210 ——— 0.034 341.0 698 CTGGTACAGTCTCAATAGGG 842 63.55 0.10 0.467 −0.025 0.280 ——— 0.186 54.8 699 TGGTACAGTCTCAATAGGGC 843 65.89 1.10 0.810 0.844 0.823 ——— 0.279 47.1 700 GGTACAGTCTCAATAGGGCT 844 68.08 0.90 1.131 0.670 0.956 ——— 0.383 59.7 701 GTACAGTCTCAATAGGGCTA 845 64.73 0.70 0.640 0.496 0.586 ——— 0.425 47.0 702 TACAGTCTCAATAGGGCTAA 846 59.35 0.70 −0.149 0.496 0.096 ——— 0.425 49.3 703 ACAGTCTCAATAGGGCTAAT 847 59.91 0.70 −0.067 0.496 0.147 ——— 0.388 55.0 704 CAGTCTCAATAGGGCTAATG 848 59.29 0.70 −0.158 0.496 0.091 ——— 0.275 49.0 705 AGTCTCAATAGGGCTAATGG 849 60.62 0.90 0.037 0.670 0.278 ——— 0.220 45.7 706 GTCTCAATAGGGCTAATGGG 850 63.00 1.10 0.386 0.844 0.560 ——— 0.189 115.6 707 TCTCAATAGGGCTAATGGGA 851 61.22 0.40 0.125 0.236 0.167 ——— 0.133 50.6 708 CTCAATAGGGCTAATGGGAA 852 57.97 1.40 −0.352 1.105 0.202 ——— 0.075 48.0 709 TCAATAGGGCTAATGGGAAA 853 54.39 1.40 −0.877 1.105 −0.124 ———−0.028 50.5 710 CAATAGGGCTAATGGGAAAA 854 51.64 1.80 −1.281 1.453 −0.242 ———−0.191 44.1 711 AATAGGGCTAATGGGAAAAT 855 50.45 1.90 −1.454 1.540 −0.316 ———−0.298 43.1 712 ATAGGGCTAATGGGAAAATT 856 52.34 1.00 −1.178 0.757 −0.442 ———−0.432 45.2 713 TAGGGCTAATGGGAAAATTT 857 52.63 0.50 −1.135 0.323 −0.581 ———−0.569 47.4 714 AGGGCTAATGGGAAAATTTA 858 52.63 0.50 −1.135 0.323 −0.581 ———−0.717 50.0 715 GGGCTAATGGGAAAATTTAA 859 50.89 0.50 −1.390 0.323 −0.739 −0.867 47.8 716 GGCTAATGGGAAAATTTAAA 860 47.14 0.50 −1.940 0.323 −1.080 −1.022 50.2 717 GCTAATGGGAAAATTTAAAG 861 45.00 0.50 −2.254 0.323 −1.275 −1.096 43.0 718 CTAATGGGAAAATTTAAAGT 862 43.95 0.50 −2.408 0.323 −1.371 −1.088 57.0 719 TAATGGGAAAATTTAAAGTG 863 42.27 0.50 −2.655 0.323 −1.524 −1.072 58.7 720 AATGGGAAAATTTAAAGTGC 864 46.18 0.70 −2.081 0.496 −1.102 −1.011 183.6 721 ATGGGAAAATTTAAAGTGCA 865 48.90 1.70 −1.682 1.366 −0.524 −0.924 303.4 722 TGGGAAAATTTAAAGTGCAA 866 47.39 1.80 −1.903 1.453 −0.628 −0.837 135.7 723 GGGAAAATTTAAAGTGCAAC 867 47.84 1.60 −1.838 1.279 −0.653 −0.766 241.7 724 GGAAAATTTAAAGTGCAACC 868 49.12 1.20 −1.649 0.931 −0.669 −0.737 132.5 725 GAAAATTTAAAGTGCAACCA 869 48.09 1.20 −1.801 0.931 −0.763 −0.758 128.8 726 AAAATTTAAAGTGCAACCAA 870 45.57 1.10 −2.171 0.844 −1.025 ———−0.720 141.0 727 AAATTTAAAGTGCAACCAAT 871 46.97 1.10 −1.965 0.844 −0.897 ———−0.679 282.0 728 AATTTAAAGTGCAACCAATC 872 49.46 1.10 −1.599 0.844 −0.671 ———−0.629 948.6 729 ATTTAAAGTGCAACCAATCT 873 52.84 1.10 −1.104 0.844 −0.363 ———−0.567 1815.1 730 TTTAAAGTGCAACCAATCTG 874 52.81 1.10 −1.109 0.844 −0.366 ———−0.426 3188.2 731 TTAAAGTGCAACCAATCTGA 875 53.71 1.00 −0.976 0.757 −0.317 ———−0.262 3566.1 732 TAAAGTGCAACCAATCTGAG 876 53.56 1.00 −0.999 0.757 −0.331 ———−0.087 2925.1 733 AAAGTGCAACCAATCTGAGT 877 56.81 1.00 −0.522 0.757 −0.036 ——— 0.014 3233.2 734 AAGTGCAACCAATCTGAGTC 878 59.99 1.00 −0.055 0.757 0.254 ——— 0.085 3615.6 735 AGTGCAACCAATCTGAGTCA 879 63.25 1.00 0.422 0.757 0.550 ——— 0.165 3994.8 736 GTGCAACCAATCTGAGTCAA 880 61.00 1.00 0.093 0.757 0.345 ——— 0.138 4033.0 737 TGCAACCAATCTGAGTCAAC 881 58.62 1.00 −0.257 0.757 0.128 ——— 0.008 3380.2 738 GCAACCAATCTGAGTCAACA 882 59.87 1.00 −0.073 0.757 0.242 ———−0.173 4288.7 739 CAACCAATCTGAGTCAACAG 883 56.22 −0.30 −0.608 −0.373 −0.519 ———−0.445 744.1 740 AACCAATCTGAGTCAACAGA 884 56.24 −1.60 −0.605 −1.504 −0.946 −0.757 392.2 741 ACCAATCTGAGTCAACAGAT 885 58.10 −2.30 −0.332 −2.112 −1.009 −1.030 158.1 742 CCAATCTGAGTCAACAGATT 886 57.90 −3.30 −0.362 −2.982 −1.357 −1.219 70.8 743 CAATCTGAGTCAACAGATTT 887 54.41 −3.80 −0.874 −3.417 −1.840 −1.262 190.0 744 AATCTGAGTCAACAGATTTC 888 54.37 −3.60 −0.880 −3.243 −1.778 −1.168 87.7 745 ATCTGAGTCAACAGATTTCT 889 58.37 −2.60 −0.293 −2.373 −1.084 −1.017 152.7 746 TCTGAGTCAACAGATTTCTT 890 58.73 −1.90 −0.241 −1.764 −0.820 −0.797 270.5 747 CTGAGTCAACAGATTTCTTC 891 58.73 −0.30 −0.241 −0.373 −0.291 ———−0.553 498.7 748 TGAGTCAACAGATTTCTTCC 892 60.70 0.20 0.049 0.062 0.054 ———−−0.321 891.0 749 GAGTCAACAGATTTCTTCCA 893 62.06 0.20 0.248 0.062 0.177 ———−0.221 1509.8 750 AGTCAACAGATTTCTTCCAA 894 58.66 0.20 −0.250 0.062 −0.132 ———−0.182 1009.3 751 GTCAACAGATTTCTTCCAAT 895 58.47 0.20 −0.279 0.062 −0.149 ———−0.235 1198.0 752 TCAACAGATTTCTTCCAATT 896 55.86 0.20 −0.661 0.062 −0.387 ———−0.315 680.5 753 CAACAGATTTCTTCCAATTA 897 54.08 0.20 −0.922 0.062 −0.548 ———−0.381 762.5 754 AACAGATTTCTTCCAATTAT 898 52.82 0.20 −1.107 0.062 −0.663 ———−0.415 689.8 755 ACAGATTTCTTCCAATTATG 899 54.58 0.20 −0.849 0.062 −0.503 ———−0.445 715.1 756 CAGATTTCTTCCAATTATGT 900 56.99 0.20 −0.496 0.062 −0.284 ———−0.460 833.8 757 AGATTTCTTCCAATTATGTT 901 56.02 0.20 −0.638 0.062 −0.372 ———−0.445 1067.7 758 GATTTCTTCCAATTATGTTG 902 55.80 0.30 −0.670 0.149 −0.359 ———−0.401 1225.9 759 ATTTCTTCCAATTATGTTGA 903 55.80 −0.10 −0.670 −0.199 −0.491 ———−0.382 1028.7 760 TTTCTTCCAATTATGTTGAC 904 56.34 −0.10 −0.591 −0.199 −0.442 ———−0.378 1419.0 761 TTCTTCCAATTATGTTGACA 905 57.29 −0.10 −0.452 −0.199 −0.356 ———−0.348 1437.4 762 TCTTCCAATTATGTTGACAG 906 57.14 −0.10 −0.474 −0.199 −0.369 ———−0.325 1518.3 763 CTTCCAATTATGTTGACAGG 907 58.36 −0.10 −0.295 −0.199 −0.259 ———−0.262 1560.3 764 TTCCAATTATGTTGACAGGT 908 59.43 −0.10 −0.138 −0.199 −0.161 ———−0.244 1100.0 765 TCCAATTATGTTGACAGGTG 909 59.02 −0.10 −0.198 −0.199 −0.198 ———−0.216 1096.4 766 CCAATTATGTTGACAGGTGT 910 60.68 −0.10 0.046 −0.199 −0.047 ———−0.124 1103.4 767 CAATTATGTTGACAGGTGTA 911 56.24 0.30 −0.605 0.149 −0.319 ———−0.005 738.1 768 AATTATGTTGACAGGTGTAG 912 55.09 1.10 −0.774 0.844 −0.159 ——— 0.054 596.7 769 ATTATGTTGACAGGTGTAGG 913 59.83 1.10 −0.079 0.844 0.272 ——— 0.161 548.1 770 TTATGTTGACAGGTGTAGGT 914 63.16 1.10 0.409 0.844 0.575 ——— 0.274 701.1 771 TATGTTGACAGGTGTAGGTC 915 64.38 −0.20 0.588 −0.286 0.256 ——— 0.420 724.7 772 ATGTTGACAGGTGTAGGTCC 916 69.08 −0.60 1.278 −0.634 0.551 ——— 0.506 1129.8 773 TGTTGACAGGTGTAGGTCCT 917 71.21 −0.60 1.591 −0.634 0.745 ——— 0.537 1214.0 774 GTTGACAGGTGTAGGTCCTA 918 70.75 −0.60 1.523 −0.634 0.703 ——— 0.520 1425.4 775 TTGACAGGTGTAGGTCCTAC 919 67.83 −0.60 1.095 −0.634 0.438 ——— 0.499 838.8 776 TGACAGGTGTAGGTCCTACT 920 69.52 −0.90 1.343 −0.895 0.493 ——— 0.427 1173.1 777 GACAGGTGTAGGTCCTACTA 921 69.06 −0.90 1.275 −0.895 0.450 ——— 0.304 1367.0 778 ACAGGTGTAGGTCCTACTAA 922 65.30 −0.90 0.723 −0.895 0.108 ——— 0.192 872.0 779 CAGGTGTAGGTCCTACTAAT 923 64.69 −0.90 0.634 −0.895 0.053 ——— 0.109 897.6 780 AGGTGTAGGTCCTACTAATA 924 62.84 −0.90 0.362 −0.895 −0.115 ———−0.024 962.2 781 GGTGTAGGTCCTACTAATAC 925 63.19 −0.90 0.414 −0.895 −0.083 ———−0.090 1382.6 782 GTGTAGGTCCTACTAATACT 926 62.53 −0.90 0.317 −0.895 −0.143 ———−0.099 1132.9 783 TGTAGGTCCTACTAATACTG 927 59.27 −0.90 −0.160 −0.895 −0.439 ———−0.095 1180.7 784 GTAGGTCCTACTAATACTGT 928 62.53 −0.50 0.317 −0.547 −0.011 ———−0.020 1932.9 785 TAGGTCCTACTAATACTGTA 929 58.77 0.70 −0.234 0.496 0.043 ——— 0.042 1634.4 786 AGGTCCTACTAATACTGTAC 930 59.91 0.50 −0.067 0.323 0.081 ——— 0.067 2488.1 787 GGTCCTACTAATACTGTACC 931 63.54 0.50 0.466 0.323 0.411 ——— 0.116 3560.9 788 GTCCTACTAATACTGTACCT 932 62.91 0.50 0.373 0.323 0.354 ——— 0.048 3850.1 789 TCCTACTAATACTGTACCTA 933 59.31 0.50 −0.155 0.323 0.026 ———−0.041 1879.0 790 CCTACTAATACTGTACCTAT 934 57.99 0.50 −0.348 0.323 −0.093 ———−0.053 1920.4 791 CTACTAATACTGTACCTATA 935 53.68 0.50 −0.981 0.323 −0.486 ———−0.094 1131.2 792 TACTAATACTGTACCTATAG 936 51.92 0.70 −1.240 0.496 −0.580 ———−0.147 756.5 793 ACTAATACTGTACCTATAGC 937 56.45 1.20 −0.574 0.931 −0.002 ———−0.142 1881.3 794 CTAATACTGTACCTATAGCT 938 57.85 1.20 −0.369 0.931 0.125 ———−0.102 2033.6 795 TAATACTGTACCTATAGCTT 939 56.25 1.20 −0.604 0.931 −0.021 ———−0.006 1853.9 796 AATACTGTACCTATAGCTTT 940 57.14 1.20 −0.473 0.931 0.060 ——— 0.111 2462.6 797 ATACTGTACCTATAGCTTTA 941 58.55 1.20 −0.266 0.931 0.189 ——— 0.183 2436.8 798 TACTGTACCTATAGCTTTAT 942 58.55 1.20 −0.266 0.931 0.189 ——— 0.220 1865.2 799 ACTGTACCTATAGCTTTATG 943 59.06 1.20 −0.192 0.931 0.235 ——— 0.331 1682.1 800 CTGTACCTATAGCTTTATGT 944 61.64 1.30 0.187 1.018 0.503 ——— 0.405 1551.3 801 TGTACCTATAGCTTTATGTC 945 61.08 1.10 0.105 0.844 0.386 ——— 0.484 1600.1 802 GTACCTATAGCTTTATGTCC 946 65.16 1.10 0.703 0.844 0.757 ——— 0.572 4094.6 803 TACCTATAGCTTTATGTCCA 947 63.16 1.10 0.409 0.844 0.575 ——— 0.597 2794.2 804 ACCTATAGCTTTATGTCCAC 948 64.30 1.30 0.577 1.018 0.745 ——— 0.575 4754.9 805 CCTATAGCTTTATGTCCACA 949 64.94 1.30 0.671 1.018 0.803 ——— 0.554 4185.4 806 CTATAGCTTTATGTCCACAG 950 61.34 1.10 0.143 0.844 0.409 ——— 0.484 3284.3 807 TATAGCTTTATGTCCACAGA 951 60.70 1.10 0.048 0.844 0.351 ——— 0.453 2819.7 808 ATAGCTTTATGTCCACAGAT 952 61.27 0.60 0.132 0.410 0.238 ——— 0.414 3545.1 809 TAGCTTTATGTCCACAGATT 953 61.63 0.60 0.186 0.410 0.271 ——— 0.337 4232.6 810 AGCTTTATGTCCACAGATTT 954 62.57 0.60 0.324 0.410 0.356 ——— 0.283 5252.8 811 GCTTTATGTCCACAGATTTC 955 63.85 0.60 0.511 0.410 0.472 ——— 0.232 6823.9 812 CTTTATGTCCACAGATTTCT 956 61.56 0.60 0.176 0.410 0.265 ——— 0.193 4829.8 813 TTTATGTCCACAGATTTCTA 957 58.97 0.60 −0.205 0.410 0.029 ——— 0.173 4333.7 814 TTATGTCCACAGATTTCTAT 958 58.62 0.60 −0.257 0.410 −0.004 ——— 0.144 3801.0 815 TATGTCCACAGATTTCTATG 959 58.20 0.60 −0.318 0.410 −0.041 ——— 0.142 3528.2 816 ATGTCCACAGATTTCTATGA 960 60.12 0.60 −0.036 0.410 0.134 ——— 0.129 2080.0 817 TGTCCACAGATTTCTATGAG 961 60.34 0.60 −0.004 0.410 0.153 ——— 0.145 913.8 818 GTCCACAGATTTCTATGAGT 962 63.68 0.60 0.486 0.410 0.457 ——— 0.122 1228.3 819 TCCACAGATTTCTATGAGTA 963 59.83 0.80 −0.078 0.583 0.173 ——— 0.067 238.1 820 CCACAGATTTCTATGAGTAT 964 58.43 1.10 −0.285 0.844 0.144 ———−0.078 219.4 821 CACAGATTTCTATGAGTATC 965 55.78 0.90 −0.673 0.670 −0.162 ———−0.169 138.6 822 ACAGATTTCTATGAGTATCT 966 56.48 −0.10 −0.571 −0.199 −0.430 ———−0.273 112.7 823 CAGATTTCTATGAGTATCTG 967 55.85 −1.30 −0.663 −1.243 −0.883 ———−0.327 133.8 824 AGATTTCTATGAGTATCTGA 968 55.87 −0.10 −0.659 −0.199 −0.485 ———−0.387 296.8 825 GATTTCTATGAGTATCTGAT 969 55.69 0.60 −0.686 0.410 −0.270 ———−0.442 279.7 826 ATTTCTATGAGTATCTGATC 970 55.67 0.80 −0.689 0.583 −0.206 ———−0.498 484.4 827 TTTCTATGAGTATCTGATCA 971 57.06 0.20 −0.485 0.062 −0.277 ———−0.510 502.0 828 TTCTATGAGTATCTGATCAT 972 56.70 −0.50 −0.538 −0.547 −0.541 ———−0.569 637.3 829 TCTATGAGTATCTGATCATA 973 55.75 −1.10 −0.678 −1.069 −0.826 ———−0.657 489.0 830 CTATGAGTATCTGATCATAC 974 54.95 −1.30 −0.794 −1.243 −0.965 ———−0.712 808.7 831 TATGAGTATCTGATCATACT 975 54.95 −1.10 −0.794 −1.069 −0.899 ———−0.738 903.2 832 ATGAGTATCTGATCATACTG 976 55.49 −1.20 −0.715 −1.156 −0.883 ———−0.707 1709.3 833 TGAGTATCTGATCATACTGT 977 58.64 −1.20 −0.254 −1.156 −0.597 ———−0.601 2103.9 834 GAGTATCTGATCATACTGTC 978 60.20 −1.20 −0.025 −1.156 −0.455 ———−0.468 3973.4 835 AGTATCTGATCATACTGTCT 979 60.88 −1.00 0.076 −0.982 −0.326 ———−0.330 6462.3 836 GTATCTGATCATACTGTCTT 980 61.03 −0.30 0.097 −0.373 −0.081 ———−0.167 9749.0 837 TATCTGATCATACTGTCTTA 981 57.16 0.90 −0.470 0.670 −0.037 ———−0.059 7817.2 838 ATCTGATCATACTGTCTTAC 982 58.34 0.90 −0.298 0.670 0.070 ——— 0.007 9683.1 539 TCTGATCATACTGTCTTACT 983 60.42 0.90 0.008 0.670 0.259 ——— 0.055 8089.0 840 CTGATCATACTGTCTTACTT 984 59.32 0.90 −0.154 0.670 0.159 ——— 0.067 8696.8 841 TGATCATACTGTCTTACTTT 985 57.63 0.90 −0.401 0.670 0.006 ——— 0.064 6880.5 842 GATCATACTGTCTTACTTTG 986 57.63 0.90 −0.401 0.670 0.006 ——— 0.020 7033.7 843 ATCATACTGTCTTACTTTGA 987 57.63 0.90 −0.401 0.670 0.006 ———−0.093 5406.5 844 TCATACTGTCTTACTTTGAT 988 57.63 0.70 −0.401 0.496 −0.060 ———−0.215 4239.4 845 CATACTGTCTTACTTTGATA 989 55.68 0.70 −0.688 0.496 −0.238 ———−0.378 3727.4 846 ATACTGTCTTACTTTGATAA 990 52.44 0.70 −1.163 0.496 −0.533 ———−0.550 2665.5 847 TACTGTCTTACTTTGATAAA 991 50.65 0.70 −1.426 0.496 −0.696 ———−0.696 1817.8 848 ACTGTCTTACTTTGATAAAA 992 49.49 −0.30 −1.595 −0.373 −1.131 −0.809 1335.9 849 CTGTCTTACTTTGATAAAAC 993 49.49 −0.50 −1.595 −0.547 −1.197 −0.916 1526.2 850 TGTCTTACTTTGATAAAACC 994 51.45 −0.50 −1.309 −0.547 −1.019 −0.949 822.7 851 GTCTTACTTTGATAAAACCT 995 53.32 −0.50 −1.034 −0.547 −0.849 −0.966 1227.4 852 TCTTACTTTGATAAAACCTC 996 51.75 −0.50 −1.264 −0.547 −0.991 −0.946 503.0 853 CTTACTTTGATAAAACCTCC 997 54.28 −0.50 −0.894 −0.547 −0.762 −0.910 1174.3 854 TTACTTTGATAAAACCTCCA 998 53.70 −0.50 −0.978 −0.547 −0.814  −0.901 885.5 855 TACTTTGATAAAACCTCCAA 999 51.79 −0.50 −1.259 −0.547 −0.988 −0.916 650.6 856 ACTTTGATAAAACCTCCAAT 1000  52.29 −0.50 −1.185 −0.547 −0.943 −0.826 615.4 857 CTTTGATAAAACCTCCAATT 1001  52.11 −0.50 −1.212 −0.547 −0.959 ———−0.728 563.4 858 TTTGATAAAACCTCCAATTC 1002  51.46 −0.30 −1.307 −0.373 −0.952 ———−0.561 420.9 859 TTGATAAAACCTCCAATTCC 1003  54.68 0.60 −0.834 0.410 −0.362 ———−0.298 536.6 860 TGATAAAACCTCCAATTCCC 1004  57.79 0.60 −0.378 0.410 −0.079 ———−0.022 1417.8 861 GATAAAACCTCCAATTCCCC 1005  61.15 1.00 0.114 0.757 0.359 ——— 0.258 4351.2 862 ATAAAACCTCCAATTCCCCC 1006  63.24 1.90 0.421 1.540 0.846 ——— 0.560 7738.7 863 TAAAACCTCCAATTCcCCCT 1007  64.88 1.90 0.663 1.540 0.996 ——— 0.817 11136.0 864 AAAACCTCCAATTCCCCCTA 1008  64.88 1.90 0.663 1.540 0.996  1.074 14811.0 865 AAACCTCCAATTCCCCCTAT 1009  66.73 1.90 0.933 1.540 1.164  1.261 15751.0 866 AACCTCCAATTCCCCCTATC 1010  70.07 1.80 1.424 1.453 1.435  1.330 19661.0 867 ACCTCCAATTCCCCCTATCA 1011  73.21 1.80 1.883 1.453 1.720  1.335 20301.0 868 CCTCCAATTCCCCCTATCAT 1012  72.64 1.80 1.801 1.453 1.669  1.327 19376.0 869 CTCCAATTCCCCCTATCATT 1013  69.66 1.60 1.364 1.279 1.332  1.254 17642.0 870 TCCAATTCCCCCTATCATTT 1014  68.21 1.10 1.150 0.844 1.034  1.093 13751.0 871 CCAATTCCCCCTATCATTTT 1015  67.12 1.10 0.991 0.844 0.935  0.931 12669.0 872 CAATTCCCCCTATCATTTTT 1016  64.02 1.10 0.536 0.844 0.653 ——— 0.818 9255.9 873 AATTCCCCCTATCATTTTTG 1017  62.80 0.40 0.357 0.236 0.311 ——— 0.753 8929.1 874 ATTCCCCCTATCATTTTTGG 1018  67.28 0.00 1.014 −0.112 0.586 ——— 0.715 6148.2 875 TTCCCCCTATCATTTTTGGT 1019  70.46 0.00 1.480 −0.112 0.875 ——— 0.664 5468.0 876 TCCCCCTATCATTTTTGGTT 1020  70.46 0.00 1.480 −0.112 0.875 ——— 0.653 5803.7 877 CCCCCTATCATTTTTGGTTT 1021  69.27 0.00 1.307 −0.112 0.768 ——— 0.658 5192.0 878 CCCCTATCATTTTTGGTTTC 1022  67.18 0.00 1.000 −0.112 0.577 ——— 0.549 3557.4 879 CCCTATCATTTTTGGTTTCC 1023  67.18 0.00 1.000 −0.112 0.577 ——— 0.392 5274.3 880 CCTATCATTTTTGGTTTCCA 1024  64.63 0.00 0.625 −0.112 0.345 ——— 0.270 3787.9 881 CTATCATTTTTGGTTTCCAT 1025  60.77 −0.50 0.059 −0.547 −0.171 ——— 0.167 2726.8 882 TATCATTTTTGGTTTCCATC 1026  60.20 −0.50 −0.025 −0.547 −0.223 ——— 0.092 3249.9 883 ATCATTTTTGGTTTCCATCT 1027  62.83 −0.50 0.361 −0.547 0.016 ——— 0.051 5548.9 884 TCATTTTTGGTTTCCATCTT 1028  63.21 −0.50 0.416 −0.547 0.050 ——— 0.071 5290.0 885 CATTTTTGGTTTCCATCTTC 1029  63.21 −0.50 0.416 −0.547 0.050 ——— 0.157 7451.0 886 ATTTTTGGTTTCCATCTTCC 1030  65.88 −0.50 0.809 −0.547 0.293 ——— 0.262 11578.0 887 TTTTTGGTTTCCATCTTCCT 1031  67.93 −0.50 1.109 −0.547 0.480 ——— 0.366 13722.0 888 TTTTGGTTTCCATCTTCCTG 1032  67.42 −0.50 1.035 −0.547 0.434 ——— 0.475 15064.0 889 TTTGGTTTCCATCTTCCTGG 1033  69.71 −0.90 1.370 −0.895 0.509 ——— 0.554 10869.0 890 TTGGTTTCCATCTTCCTGGC 1034  73.74 −1.30 1.962 −1.243 0.744 ——— 0.535 16035.0 891 TGGTTTCCATCTTCCTGGCA 1035  74.48 −1.30 2.071 −1.243 0.812 ——— 0.457 16304.0 892 GGTTTCCATCTTCCTGGCAA 1036  72.21 −1.30 1.737 −1.243 0.605 ——— 0.406 14885.0 893 GTTTCCATCTTCCTGGCAAA 1037  67.37 −1.30 1.027 −1.243 0.165 ——— 0.358 11910.0 894 TTTCCATCTTCCTGGCAAAC 1038  64.82 −1.30 0.653 −1.243 −0.067 ——— 0.290 11929.0 895 TTCCATCTTCCTGGCAAACT 1039  66.34 −1.30 0.877 −1.243 0.071 ——— 0.252 11517.0 896 TCCATCTTCCTGGCAAACTC 1040  67.47 −1.30 1.042 −1.243 0.174 ——— 0.237 11822.0 897 CCATCTTCCTGGCAAACTCA 1041  67.12 −0.90 0.991 −0.895 0.274 ——— 0.285 11710.0 898 CATCTTCCTGGCAAACTCAT 1042  63.55 0.90 0.466 0.670 0.544 ——— 0.357 7635.3 899 ATCTTCCTGGCAAACTCATT 1043  62.71 1.00 0.343 0.757 0.501 ——— 0.409 8378.2 900 TCTTCCTGGCAAACTCATTT 1044  63.06 0.90 0.395 0.670 0.500 ——— 0.446 6321.4 901 CTTCCTGGCAAACTCATTTC 1045  63.06 0.70 0.395 0.496 0.434 ——— 0.468 7659.0 902 TTCCTGGCAAACTCATTTCT 1046  63.06 0.70 0.395 0.496 0.434 ——— 0.429 11621.0 903 TCCTGGCAAACTCATTTCTT 1047  63.06 0.70 0.395 0.496 0.434 ——— 0.363 3389.0 904 CCTGGCAAACTCATTTCTTC 1048  63.06 0.70 0.395 0.496 0.434 ——— 0.273 3870.6 905 CTGGCAAACTCATTTCTTCT 1049  61.24 0.70 0.127 0.496 0.268 ——— 0.160 1992.7 906 TGGCAAACTCATTTCTTCTA 1050  58.74 0.70 −0.239 0.496 0.040 ———−0.015 698.3 907 GGCAAACTCATTTCTTCTAA 1051  56.86 0.70 −0.514 0.496 −0.130 ———−0.201 718.3 908 GCAAACTCATTTCTTCTAAT 1052  54.36 0.70 −0.882 0.496 −0.358 ———−0.339 372.3 909 CAAACTCATTTCTTCTAATA 1053  49.93 0.60 −1.530 0.410 −0.793 ———−0.430 180.6 910 AAACTCATTTCTTCTAATAC 1054  49.11 0.60 −1.651 0.410 −0.868 ———−0.455 430.0 911 AACTCATTTCTTCTAATACT 1055  52.79 0.60 −1.111 0.410 −0.533 ———−0.491 904.3 912 ACTCATTTCTTCTAATACTG 1056  54.63 0.60 −0.842 0.410 −0.366 ———−0.510 1663.5 913 CTCATTTCTTCTAATACTGT 1057  57.14 0.60 −0.474 0.410 −0.138 ———−0.459 2694.2 914 TCATTTCTTCTAATACTGTA 1058  54.51 0.60 −0.859 0.410 −0.377 ———−0.361 3222.9 915 CATTTCTTCTAATACTGTAT 1059  53.21 0.60 −1.049 0.410 −0.495 ———−0.310 3142.8 916 ATTTCTTCTAATACTGTATC 1060  53.13 0.80 −1.061 0.583 −0.436 ———−0.270 5867.0 917 TTTCTTCTAATACTGTATCA 1061  54.51 1.20 −0.859 0.931 −0.179 ———−0.253 6641.4 918 TTCTTCTAATACTGTATCAT 1062  54.17 1.30 −0.908 1.018 −0.176 ———−0.229 7151.9 919 TCTTCTAATACTGTATCATC 1063  55.17 1.30 −0.762 1.018 −0.086 ———−0.139 8134.9 920 CTTCTAATACTGTATCATCT 1064  55.86 1.30 −0.661 1.018 −0.023 ———−0.048 8551.4 921 TTCTAATACTGTATCATCTG 1065  53.80 1.30 −0.964 1.018 −0.211 ———−0.003 5741.7 922 TCTAATACTGTATCATCTGC 1066  57.65 1.30 −0.398 1.018 0.140 ——— 0.101 8575.9 923 CTAATACTGTATCATCTGCT 1067  58.28 1.30 −0.307 1.018 0.197 ——— 0.248 8980.3 924 TAATACTGTATCATCTGCTC 1068  57.65 1.30 −0.398 1.018 0.140 ——— 0.384 10762.0 925 AATACTGTATCATCTGCTCC 1069  62.19 1.30 0.268 1.018 0.553 ——— 0.566 17037.0 926 ATACTGTATCATCTGCTCCT 1070  66.43 1.30 0.889 1.018 0.938 ——— 0.682 20970.0 927 TACTGTATCATCTGCTCCTG 1071  66.32 1.30 0.874 1.018 0.929 ——— 0.763 23084.0 928 ACTGTATCATCTGCTCCTGT 1072  70.36 0.60 1.466 0.410 1.065  0.875 24474.0 929 CTGTATCATCTGCTCCTGTA 1073  69.13 0.60 1.286 0.410 0.953  0.910 22217.0 930 TGTATCATCTGCTCCTGTAT 1074  67.04 0.60 0.979 0.410 0.763  0.890 19829.0 931 GTATCATCTGCTCCTGTATC 1075  68.85 0.60 1.244 0.410 0.927  0.842 23548.0 932 TATCATCTGCTCCTGTATCT 1076  67.44 0.60 1.037 0.410 0.799 ——— 0.773 21759.0 933 ATCATCTGCTCCTGTATCTA 1077  67.44 0.60 1.037 0.410 0.799 ——— 0.725 22711.0 934 TCATCTGCTCCTGTATCTAA 1078  65.13 0.60 0.699 0.410 0.589 ——— 0.706 18134.0 935 CATCTGCTCCTGTATCTAAT 1079  63.60 1.00 0.475 0.757 0.582 ——— 0.611 17772.0 936 ATCTGCTCCTGTATCTAATA 1080  61.77 1.60 0.207 1.279 0.614 ——— 0.502 17134.0 937 TCTGCTCCTGTATCTAATAG 1081  62.01 1.60 0.241 1.279 0.635 ——— 0.389 10969.0 938 CTGCTCCTGTATCTAATAGA 1082  61.90 0.50 0.225 0.323 0.262 ——— 0.336 9556.3 939 TGCTCCTGTATCTAATAGAG 1083  60.12 0.30 −0.036 0.149 0.034 ——— 0.264 3739.9 940 GCTCCTGTATCTAATAGAGC 1084  64.50 −1.00 0.607 −0.982 0.003 ——— 0.187 4088.3 941 CTCCTGTATCTAATAGAGCT 1085  62.21 0.30 0.271 0.149 0.224 ——— 0.106 2263.0 942 TCCTGTATCTAATAGAGCTT 1086  60.56 0.30 0.028 0.149 0.074 ——— 0.080 1018.0 943 CCTGTATCTAATAGAGCTTC 1087  60.56 0.30 0.028 0.149 0.074 ——— 0.091 1319.1 944 CTGTATCTAATAGAGCTTCC 1088  60.56 0.30 0.028 0.149 0.074 ——— 0.070 2347.8 945 TGTATCTAATAGAGCTTCCT 1089  60.56 0.30 0.028 0.149 0.074 ——— 0.018 1871.6 946 GTATCTAATAGAGCTTCCTT 1090  61.00 0.30 0.092 0.149 0.114 ———−0.010 3469.1 947 TATCTAATAGAGCTTCCTTT 1091  58.20 0.30 −0.318 0.149 −0.141 ———−0.030 1114.6 948 ATCTAATAGAGCTTCCTTTA 1092  58.20 0.30 −0.318 0.149 −0.141 ———−0.057 1358.4 949 TCTAATAGAGCTTCCTTTAG 1093  58.39 0.30 −0.289 0.149 −0.123 ———−0.078 665.4 950 CTAATAGAGCTTCCTTTAGT 1094  60.12 0.00 −0.036 −0.112 −0.065 ———−0.019 807.4 951 TAATAGAGCTTCCTTTAGTT 1095  58.46 0.30 −0.280 0.149 −0.117 ——— 0.128 608.7 952 AATAGAGCTTCCTTTAGTTG 1096  58.97 0.30 −0.205 0.149 −0.070 ——— 0.332 623.8 953 ATAGAGCTTCCTTTAGTTGC 1097  65.53 0.30 0.758 0.149 0.526 ——— 0.576 674.5 954 TAGAGCTTCCTTTAGTTGCC 1098  69.50 0.30 1.340 0.149 0.887  0.841 814.3 955 AGAGCTTCCTTTAGTTGCCC 1099  73.89 0.30 1.983 0.149 1.286  1.157 1183.8 956 GAGCTTCCTTTAGTTGCCCC 1100  77.20 0.30 2.470 0.149 1.588  1.454 2219.4 957 AGCTTCCTTTAGTTGCCCCC 1101  79.38 0.30 2.789 0.149 1.785  1.650 4642.2 958 GCTTCCTTTAGTTGCCCCCC 1102  82.41 0.40 3.234 0.236 2.095  1.765 8804.8 959 CTTCCTTTAGTTGCCCCCCT 1103  80.06 0.80 2.889 0.583 2.013  1.823 11331.0 960 TTCCTTTAGTTGCCCCCCTA 1104  77.67 1.10 2.539 0.844 1.895  1.818 12976.0 961 TCCTTTAGTTGCCCCCCTAT 1105  77.27 0.60 2.480 0.410 1.693  1.765 12369.0 962 CCTTTAGTTGCCCCCCTATC 1106  77.27 0.60 2.480 0.410 1.693  1.669 15090.0 963 CTTTAGTTGCCCCCCTATCT 1107  75.74 0.60 2.255 0.410 1.554  1.581 16130.0 964 TTTAGTTGCCCCCCTATCTT 1108  74.23 0.60 2.033 0.410 1.416  1.545 15304.0 965 TTAGTTGCCCCCCTATCTTT 1109  74.23 0.60 2.033 0.410 1.416  1.539 14829.0 966 TAGTTGCCCCCCTATCTTTA 1110  73.31 0.80 1.899 0.583 1.399  1.490 15309.0 967 AGTTGCCCCCCTATCTTTAT 1111  73.83 1.40 1.976 1.105 1.645  1.498 15205.0 968 GTTGCCCCCCTATCTTTATT 1112  73.91 1.40 1.986 1.105 1.652  1.524 14192.0 969 TTGCCCCCCTATCTTTATTG 1113  70.59 1.40 1.500 1.105 1.350  1.515 8699.5 970 TGCCCCCCTATCTTTATTGT 1114  73.39 1.40 1.911 1.105 1.605  1.461 7786.6 971 GCCCCCCTATCTTTATTGTG 1115  73.39 1.40 1.911 1.105 1.605  1.328 6709.1 972 CCCCCCTATCTTTATTGTGA 1116  70.61 1.40 1.502 1.105 1.351  1.165 6198.4 973 CCCCCTATCTTTATTGTGAC 1117  67.66 1.20 1.070 0.931 1.017  0.999 4910.2 974 CCCCTATCTTTATTGTGACG 1118  64.37 1.20 0.587 0.931 0.718 ——— 0.780 850.0 975 CCCTATCTTTATTGTGACGA 1119  62.05 1.20 0.248 0.931 0.507 ——— 0.570 404.9 976 CCTATCTTTATTGTGACGAG 1120  58.56 1.20 −0.265 0.931 0.190 ——— 0.436 166.6 977 CTATCTTTATTGTGACGAGG 1121  57.28 1.20 −0.452 0.931 0.073 ——— 0.376 126.9 978 TATCTTTATTGTGACGAGGG 1122  57.91 1.20 −0.361 0.931 0.130 ——— 0.279 92.6 979 ATCTTTATTGTGACGAGGGG 1123  61.03 1.20 0.097 0.931 0.414 ——— 0.173 97.9 980 TCTTTATTGTGACGAGGGGT 1124  64.18 0.90 0.559 0.670 0.601 ——— 0.097 122.3 981 CTTTATTGTGACGAGGGGTC 1125  64.18 −0.80 0.559 −0.808 0.039 ——— 0.013 267.0 982 TTTATTGTGACGAGGGGTCG 1126  62.63 −1.20 0.332 −1.156 −0.233 ———−0.073 396.0 983 TTATTGTGACGAGGGGTCGT 1127  65.37 −2.30 0.734 −2.112 −0.348 ———−0.145 446.0 984 TATTGTGACGAGGGGTCGTT 1128  65.37 −2.80 0.734 −2.547 −0.513 ———−0.202 661.9 985 ATTGTGACGAGGGGTCGTTG 1129  65.82 −2.80 0.800 −2.547 −0.472 ———−0.163 864.5 986 TTGTGACGAGGGGTCGTTGC 1130  70.01 −2.80 1.414 −2.547 −0.091 ———−0.156 1465.7 987 TGTGACGAGGGGTCGTTGCC 1131  73.21 −2.80 1.884 −2.547 0.200 ———−0.157 2836.9 988 GTGACGAGGGGTCGTTGCCA 1132  74.44 −2.80 2.065 −2.547 0.312 ———−0.137 3589.7 989 TGACGAGGGGTCGTTGCCAA 1133  69.05 −2.80 1.274 −2.547 −0.178 ———−0.058 2100.4 990 GACGAGGGGTCGTTGCCAAA 1134  67.10 −2.80 0.988 −2.547 −0.355 ——— 0.042 1948.7 991 ACGAGGGGTCGTTGCCAAAG 1135  66.13 −2.60 0.845 −2.373 −0.378 ——— 0.125 1384.3 992 CGAGGGGTCGTTGCCAAAGA 1136  66.81 −1.40 0.945 −1.330 0.081 ——— 0.187 1192.0 993 GAGGGGTCGTTGCCAAAGAG 1137  66.84 0.20 0.950 0.062 0.612 ——— 0.304 1221.0 994 AGGGGTCGTTGCCAAAGAGT 1138  68.70 0.20 1.223 0.062 0.782 ——— 0.427 953.2 995 GGGGTCGTTGCCAAAGAGTG 1139  68.32 0.20 1.167 0.062 0.747 ——— 0.515 988.6 996 GGGTCGTTGCCAAAGAGTGA 1140  67.11 0.20 0.989 0.062 0.636 ——— 0.476 937.8 997 GGTCGTTGCCAAAGAGTGAT 1141  64.59 0.50 0.620 0.323 0.507 ——— 0.333 852.1 998 GTCGTTGCCAAAGAGTGATC 1142  63.51 0.00 0.461 −0.112 0.243 ——— 0.176 1189.4 999 TCGTTGCCAAAGAGTGATCT 1143  62.35 −1.00 0.291 −0.982 −0.192 ———−0.012 1501.7 1000  CGTTGCCAAAGAGTGATCTG 1144  60.92 −1.20 0.081 −1.156 −0.389 ———−0.156 1360.9 1001  GTTGCCAAAGAGTGATCTGA 1145  61.71 −1.20 0.198 −1.156 −0.317 ———−0.263 1112.9 1002  TTGCCAAAGAGTGATCTGAG 1146  58.90 −1.20 −0.215 −1.156 −0.572 ———−0.353 468.3 1003  TGCCAAAGAGTGATCTGAGG 1147  61.08 −1.20 0.104 −1.156 −0.375 ———−0.454 400.1 1004  GCCAAAGAGTGATCTGAGGG 1148  63.68 −1.50 0.485 −1.417 −0.237 ———−0.541 401.6 1005  CCAAAGAGTGATCTGAGGGA 1149  60.94 −1.20 0.084 −1.156 −0.387 ———−0.575 199.9 1006  CAAAGAGTGATCTGAGGGAA 1150  55.32 −1.20 −0.741 −1.156 −0.899 ———−0.530 202.1 1007  AAAGAGTGATCTGAGGGAAG 1151  54.21 −1.20 −0.903 −1.156 −0.999 ———−0.491 258.7 1008  AAGAGTGATCTGAGGGAAGT 1152  59.12 −1.20 −0.183 −1.156 −0.552 ———−0.475 274.7 1009  AGAGTGATCTGAGGGAAGTT 1153  61.60 −1.00 0.181 −0.982 −0.261 ———−0.463 297.2 1010  GAGTGATCTGAGGGAAGTTA 1154  60.78 −0.30 0.061 −0.373 −0.104 ———−0.414 250.6 1011  AGTGATCTGAGGGAAGTTAA 1155  57.35 0.60 −0.443 0.410 −0.119 ———−0.318 231.3 1012  GTGATCTGAGGGAAGTTAAA 1156  55.25 0.60 −0.751 0.410 −0.310 ———−0.286 214.5 1013  TGATCTGAGGGAAGTTAAAG 1157  52.55 0.60 −1.147 0.410 −0.556 ———−0.295 102.3 1014  GATCTGAGGGAAGTTAAAGG 1158  55.09 0.60 −0.774 0.410 −0.324 ———−0.330 102.3 1015  ATCTGAGGGAAGTTAAAGGA 1159  55.09 0.60 −0.774 0.410 −0.324 ———−0.367 49.4 1016  TCTGAGGGAAGTTAAAGGAT 1160  55.09 0.60 −0.774 0.410 −0.324 ———−0.379 104.3 1017  CTGAGGGAAGTTAAAGGATA 1161  53.32 1.00 −1.034 0.757 −0.353 ———−0.370 46.3 1018  TGAGGGAAGTTAAAGGATAC 1162  51.95 1.30 −1.235 1.018 −0.378 ———−0.360 50.9 1019  GAGGGAAGTTAAAGGATACA 1163  53.26 0.90 −1.043 0.670 −0.392 58.2 1020  AGGGAAGTTAAAGGATACAG 1164  52.14 0.90 −1.207 0.670 −0.494 50.5 1021  GGGAAGTTAAAGGATACAGT 1165  54.81 0.90 −0.815 0.670 −0.251 53.1

Example 3

Synopsis:

The method of the present invention is particularly useful as a guide to the iterative refinement of probes. One of the specific predictions made for rabbit β-globin in Example 1 is used to provide an example of such a refinement.

Materials and Methods:

The contig spanning positions 5-11 of a portion of the rabbit β-globin gene (Example 1, Table 3) was analyzed, using the experimentally measured data to simulate the results of successive experimental measurements. The iterative refinement was performed using a rule-based algorithm, outlined below. This algorithm is used by way of example only; other algorithms for efficiently finding local maxima are well known to the art and could be employed to perform this task.

Given experimental data for probes from the 1^(st) quartile, median and 3^(rd) quartile of a contig, as well as a user-set signal threshold for further consideration of a probe,

1) If all 3 measurements are below the user-specified signal threshold, discard the prediction.

2) If at least one of the measurements is above the user-specified threshold, determine which point yields the maximum signal.

a) If the maximum point is the 1^(st) quartile probe, then make three new measurements for probes with the same spacing as that used in the preceding iteration, but displaced so that the third probe is identical to the original 1^(st) quartile probe. In other words, repeat the search with the same pattern and spacing, but displace the pattern in the direction of increasing signal found in the first experiment.

b) If the maximum point is the 3^(rd) quartile probe, then make three new measurements for probes with the same spacing as that used in the preceding iteration, but displaced so that the first probe is identical to the original 3^(rd) quartile probe. In other words, repeat the search with the same pattern and spacing, but displace the pattern in the direction of increasing signal found in the first experiment.

c) If the maximum point is the median probe, then repeat the experiment, keeping the median point the same, but shrinking the spacing between probes by a factor of 2.

3) Continue iteration until a maximum is found, or the user judges the signal level observed to be acceptable. Use the experimental value measured for the probe duplicated in successive iterations to tie together the successive data sets, via a simple normalization procedure, described below. Where appropriate, consider all of the data (i.e. all of the iterations) when deciding how to proceed, or whether the peak hybridization intensity has been found.

Results:

Iterative refinement of the contig spanning positions 5-11 in Table 3 proceeds as follows:

Iteration 1: Probes are synthesized at positions 6, 8 and 10, yielding the experimental hybridization intensities 180, 220 and 310, respectively.

Iteration 2: Following rule 2b), probes are synthesized at positions 10, 12 and 14. Note that the redundant measurement at position 10 serves as a bridge between experiments, and allows comparison of the two sets by normalizing the intensities by multiplying the second iteration measurements by the ratio of the intensity observed for the probe at position 10 in the first iteration to the value observed in the second iteration. In the simplest case, the ratio is 1; in any case, the second iteration yields the normalized values 310, 390, 240 for probe positions 10, 12 and 14, respectively.

Iteration 3: By rule 2c), measurements are performed for probes at positions 11, 12 and 13; after normalization, these yield the normalized hybridization intensities 320, 390 and 410, respectively. Combination of these results with the results from iteration 2, probe position 14, yields the conclusion that the best probe for this intensity peak is the probe that starts at sequence position 13. The overall result is that iterative improvement converges in three iterations, and requires the synthesis of seven test probes, one of which is the local optimal probe. In addition, the first and second iterations yield probes that exhibit 75% and 95% of the local maximum hybridization intensities, respectively. In many applications, either of these probes would be considered acceptable.

The above examples 1 and 2 demonstrate that two different implementations of the method of the present invention are capable of efficiently predicting regions of high hybridization efficiency in a variety of polynucleotide targets. Many of the predictions yield acceptable probe sequences on the first design iteration, and all would yield optimized probe sets after 2-4 rounds of iterative refinement, as demonstrated in Example 3. The performance demonstrated in these examples greatly exceeds the performance of current methods. Finally, the examples demonstrate that the predictions can be performed by a software application that has been implemented and installed on a Pentium®-based computer workstation.

All publications and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference.

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be readily apparent to those of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims.

1165 24 base pairs nucleic acid single linear cDNA YES NO not provided stem_loop 2..21 1 ACTGGCAATC ACAATTGCCA GTAA 24 75 base pairs nucleic acid single linear tRNA NO NO Saccharomyces cerevisiae tRNA 1..75 experimental /function= “transfer RNA” /product= “tRNA-Ala” /evidence= EXPERIMENTAL /anticodon= (pos 34 .. 36, aa Ala) /citation= ([1][2]) modified_base experimental /evidence= EXPERIMENTAL /frequency= 0.9999 /mod_base= m1g /citation= ([1][2]) modified_base 16 experimental /evidence= EXPERIMENTAL /frequency= 0.9999 /mod_base= d /citation= ([1][2]) modified_base 20 experimental /evidence= EXPERIMENTAL /frequency= 0.9999 /mod_base= d /citation= ([1][2]) modified_base 26 experimental /evidence= EXPERIMENTAL /frequency= 0.9999 /mod_base= m22g /citation= ([1][2]) modified_base 34 experimental /evidence= EXPERIMENTAL /frequency= 0.9999 /mod_base= i /citation= ([1][2]) modified_base 37 experimental /evidence= EXPERIMENTAL /frequency= 0.9999 /mod_base= m1i /citation= ([1][2]) modified_base 38 experimental /evidence= EXPERIMENTAL /frequency= 0.9999 /mod_base= p /citation= ([1][2]) modified_base 46 experimental /evidence= EXPERIMENTAL /frequency= 0.9999 /mod_base= d /citation= ([1][2]) modified_base 53 experimental /evidence= EXPERIMENTAL /frequency= 0.9999 /mod_base= t /citation= ([1][2]) modified_base 54 experimental /evidence= EXPERIMENTAL /frequency= 0.9999 /mod_base= p /citation= ([1][2]) R. W. Apgar, J. Everett, G. A. Madison, J. T. Marquisee, M. Merrill, S. H. Penswick, J. R. Zamir, A.Holley Structure of a ribonucleic acid Science 147 1462-1465 1965 2 FROM 1 TO 75 J. R. Martin, R. Dirheimer, G.Penswick Evidence supporting a revised sequence for yeast alanine tRNA FEBS Lett. 50 28-31 1975 2 FROM 1 TO 75 2 GGGCGUGUGG CGUAGUCGGU AGCGCGCUCC CUUGGCGUGG GAGAGUCUCC GGUUCGAUUC 60 CGGACUCGUC CACCA 75 16 base pairs nucleic acid single linear cDNA YES NO not provided 3 ATGGACTTAG CATTCG 16 12 base pairs nucleic acid single linear cDNA YES NO not provided 4 ATGGACTTAG CA 12 12 base pairs nucleic acid single linear cDNA YES NO not provided 5 TGGACTTAGC AT 12 12 base pairs nucleic acid single linear cDNA YES NO not provided 6 GGACTTAGCA TT 12 12 base pairs nucleic acid single linear cDNA YES NO not provided 7 GACTTAGCAT TC 12 12 base pairs nucleic acid single linear cDNA YES NO not provided 8 ACTTAGCATT CG 12 50 base pairs nucleic acid single linear cDNA YES NO not provided 9 GTCCAAAAAG GGTCAGTCTA CCTCCCGCCA TAAAAAACTC ATGTTCAAGA 50 25 base pairs nucleic acid single linear cDNA YES NO not provided 10 GTCCAAAAAG GGTCAGTCTA CCTCC 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 11 TCCAAAAAGG GTCAGTCTAC CTCCC 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 12 CCAAAAAGGG TCAGTCTACC TCCCG 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 13 CAAAAAGGGT CAGTCTACCT CCCGC 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 14 AAAAAGGGTC AGTCTACCTC CCGCC 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 15 AAAAGGGTCA GTCTACCTCC CGCCA 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 16 AAAGGGTCAG TCTACCTCCC GCCAT 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 17 AAGGGTCAGT CTACCTCCCG CCATA 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 18 AGGGTCAGTC TACCTCCCGC CATAA 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 19 GGGTCAGTCT ACCTCCCGCC ATAAA 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 20 GGTCAGTCTA CCTCCCGCCA TAAAA 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 21 GTCAGTCTAC CTCCCGCCAT AAAAA 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 22 TCAGTCTACC TCCCGCCATA AAAAA 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 23 CAGTCTACCT CCCGCCATAA AAAAC 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 24 AGTCTACCTC CCGCCATAAA AAACT 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 25 GTCTACCTCC CGCCATAAAA AACTC 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 26 TCTACCTCCC GCCATAAAAA ACTCA 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 27 CTACCTCCCG CCATAAAAAA CTCAT 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 28 TACCTCCCGC CATAAAAAAC TCATG 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 29 ACCTCCCGCC ATAAAAAACT CATGT 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 30 CCTCCCGCCA TAAAAAACTC ATGTT 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 31 CTCCCGCCAT AAAAAACTCA TGTTC 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 32 TCCCGCCATA AAAAACTCAT GTTCA 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 33 CCCGCCATAA AAAACTCATG TTCAA 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 34 CCGCCATAAA AAACTCATGT TCAAG 25 25 base pairs nucleic acid single linear cDNA YES NO not provided 35 CGCCATAAAA AACTCATGTT CAAGA 25 122 base pairs nucleic acid single linear cDNA NO NO Oryctolagus cuniculus 5′UTR 1..53 CDS 54..122 /codon_start= 54 /product= “rabbit beta1 globin, N-terminus” /citation= ([1]) M. L. III Johnson, J. E. James, M. D. Hardison, R. C.Rohrbaugh Transcriptional unit of the rabbit beta1 globin gene Mol. Cell. Biol. 5 147-160 1985 36 FROM 1 TO 122 36 ACACTTGCTT TTGACACAAC TGTGTTTACT TGCAATCCCC CAAAACAGAC AGA ATG 56 Met 1 GTG CAT CTG TCC AGT GAG GAG AAG TCT GCG GTC ACT GCC CTG TGG GGC 104 Val His Leu Ser Ser Glu Glu Lys Ser Ala Val Thr Ala Leu Trp Gly 5 10 15 AAG GTG AAT GTG GAA GAA 122 Lys Val Asn Val Glu Glu 20 1040 base pairs nucleic acid single linear cDNA NO NO Human immunodefficiency virus type I BH10 misc_RNA 1..1040 experimental /partial /function= “protease & reverse transcriptase regions” /product= “pol polyprotein (partial)” /evidence= EXPERIMENTAL /citation= ([1]) F. Gallo, R. C. Chang, N. T. Ghrayeb, J. Papas, T. S. Lautenberger, J. A. Pearson, M. L. Jr. Petteway, S. R. Ivanoff, L. Baumeister, K.Wong-Stahl Complete nucleotide sequence of the AIDS virus, HTLV-III Nature 313 277-284 1985 37 FROM 1 TO 1040 37 TGTACTGTCC ATTTATCAGG ATGGAGTTCA TAACCCATCC AAAGGAATGG AGGTTCTTTC 60 TGATGTTTTT TGTCTGGTGT GGTAAGTCCC CACCTCAACA GATGTTGTCT CAGCTCCTCT 120 ATTTTTGTTC TATGCTGCCC TATTTCTAAG TCAGATCCTA CATACAAATC ATCCATGTAT 180 TGATAGATAA CTATGTCTGG ATTTTGTTTT TTAAAAGGCT CTAAGATTTT TGTCATGCTA 240 CTTTGGAATA TTGCTGGTGA TCCTTTCCAT CCCTGTGGAA GCACATTGTA CTGATATCTA 300 ATCCCTGGTG TCTCATTGTT TATACTAGGT ATGGTAAATG CAGTATACTT CCTGAAGTCT 360 TCATCTAAGG GAACTGAAAA ATATGCATCA CCCACATCCA GTACTGTTAC TGATTTTTTC 420 TTTTTTAACC CTGCGGGATG TGGTATTCCT AATTGAACTT CCCAGAAGTC TTGAGTTCTC 480 TTATTAAGTT CTCTGAAATC TACTAATTTT CTCCATTTAG TACTGTCTTT TTTCTTTATG 540 GCAAATACTG GAGTATTGTA TGGATTCTCA GGCCCAATTT TTGAAATTTT CCCTTCCTTT 600 TCCATTTCTG TACAAATTTC TACTAATGCT TTTATTTTTT CTTCTGTCAA TGGCCATTGT 660 TTAACTTTTG GGCCATCCAT TCCTGGCTTT AATTTTACTG GTACAGTCTC AATAGGGCTA 720 ATGGGAAAAT TTAAAGTGCA ACCAATCTGA GTCAACAGAT TTCTTCCAAT TATGTTGACA 780 GGTGTAGGTC CTACTAATAC TGTACCTATA GCTTTATGTC CACAGATTTC TATGAGTATC 840 TGATCATACT GTCTTACTTT GATAAAACCT CCAATTCCCC CTATCATTTT TGGTTTCCAT 900 CTTCCTGGCA AACTCATTTC TTCTAATACT GTATCATCTG CTCCTGTATC TAATAGAGCT 960 TCCTTTAGTT GCCCCCCTAT CTTTATTGTG ACGAGGGGTC GTTGCCAAAG AGTGATCTGA 1020 GGGAAGTTAA AGGATACAGT 1040 999 base pairs nucleic acid single linear cDNA NO NO Homo sapiens CDS 1..982 experimental /partial /codon_start= 2 /function= “glycolysis” /product= “Glyceraldehydephosphate Dehydrogenase” /evidence= EXPERIMENTAL /standard_name= “G3PDH” /citation= ([1]) promoter 983..999 /function= “promoter for T7 RNA polymerase” P. Martinelli, R. Salvatore, F.Arcari The complete sequence of a full length cDNA for human liver glyceraldehyde-3-phosphate dehydrogenase evidence for multiple mRNA species Nucleic Acids Res. 12 23 9179-9189 1984 38 FROM 1 TO 999 38 G AAG GTC GGA GTC AAC GGA TTT GGT CGT ATT GGG CGC CTG GTC ACC 46 Lys Val Gly Val Asn Gly Phe Gly Arg Ile Gly Arg Leu Val Thr 1 5 10 15 AGG GCT GCT TTT AAC TCT GGT AAA GTG GAT ATT GTT GCC ATC AAT GAC 94 Arg Ala Ala Phe Asn Ser Gly Lys Val Asp Ile Val Ala Ile Asn Asp 20 25 30 CCC TTC ATT GAC CTC AAC TAC ATG GTT TAC ATG TTC CAA TAT GAT TCC 142 Pro Phe Ile Asp Leu Asn Tyr Met Val Tyr Met Phe Gln Tyr Asp Ser 35 40 45 ACC CAT GGC AAA TTC CAT GGC ACC GTC AAG GCT GAG AAC GGG AAG CTT 190 Thr His Gly Lys Phe His Gly Thr Val Lys Ala Glu Asn Gly Lys Leu 50 55 60 GTC ATC AAT GGA AAT CCC ATC ACC ATC TTC CAG GAG CGA GAT CCC TCC 238 Val Ile Asn Gly Asn Pro Ile Thr Ile Phe Gln Glu Arg Asp Pro Ser 65 70 75 AAA ATC AAG TGG GGC GAT GCT GGC GCT GAG TAC GTC GTG GAG TCC ACT 286 Lys Ile Lys Trp Gly Asp Ala Gly Ala Glu Tyr Val Val Glu Ser Thr 80 85 90 95 GGC GTC TTC ACC ACC ATG GAG AAG GCT GGG GCT CAT TTG CAG GGG GGA 334 Gly Val Phe Thr Thr Met Glu Lys Ala Gly Ala His Leu Gln Gly Gly 100 105 110 GCC AAA AGG GTC ATC ATC TCT GCC CCC TCT GCT GAT GCC CCC ATG TTC 382 Ala Lys Arg Val Ile Ile Ser Ala Pro Ser Ala Asp Ala Pro Met Phe 115 120 125 GTC ATG GGT GTG AAC CAT GAG AAG TAT GAC AAC AGC CTC AAG ATC ATC 430 Val Met Gly Val Asn His Glu Lys Tyr Asp Asn Ser Leu Lys Ile Ile 130 135 140 AGC AAT GCC TCC TGC ACC ACC AAC TGC TTA GCA CCC CTG GCC AAG GTC 478 Ser Asn Ala Ser Cys Thr Thr Asn Cys Leu Ala Pro Leu Ala Lys Val 145 150 155 ATC CAT GAC AAC TTT GGT ATC GTG GAA GGA CTC ATG ACC ACA GTC CAT 526 Ile His Asp Asn Phe Gly Ile Val Glu Gly Leu Met Thr Thr Val His 160 165 170 175 GCC ATC ACT GCC ACC CAG AAG ACT GTG GAT GGC CCC TCC GGG AAA CTG 574 Ala Ile Thr Ala Thr Gln Lys Thr Val Asp Gly Pro Ser Gly Lys Leu 180 185 190 TGG CGT GAT GGC CGC GGG GCT CTC CAG AAC ATC ATC CCT GCC TCT ACT 622 Trp Arg Asp Gly Arg Gly Ala Leu Gln Asn Ile Ile Pro Ala Ser Thr 195 200 205 GGC GCT GCC AAG GCT GTG GGC AAG GTC ATC CCT GAG CTA GAC GGG AAG 670 Gly Ala Ala Lys Ala Val Gly Lys Val Ile Pro Glu Leu Asp Gly Lys 210 215 220 CTC ACT GGC ATG GCC TTC CGT GTC CCC ACT GCC AAC GTG TCA GTG GTG 718 Leu Thr Gly Met Ala Phe Arg Val Pro Thr Ala Asn Val Ser Val Val 225 230 235 GAC CTG ACC TGC CGT CTA GAA AAA CCT GCC AAA TAT GAT GAC ATC AAG 766 Asp Leu Thr Cys Arg Leu Glu Lys Pro Ala Lys Tyr Asp Asp Ile Lys 240 245 250 255 AAG GTG GTG AAG CAG GCG TCG GAG GGC CCC CTC AAA GGC ATC CTG GGC 814 Lys Val Val Lys Gln Ala Ser Glu Gly Pro Leu Lys Gly Ile Leu Gly 260 265 270 TAC ACT GAG CAC CAG GTG GTC TCC TCT GAC TTC AAC AGC GAC ACC CAC 862 Tyr Thr Glu His Gln Val Val Ser Ser Asp Phe Asn Ser Asp Thr His 275 280 285 TCC TCC ACC TTT GAC GCT GGG GCT GGC ATT GCC CTC AAC GAC CAC TTT 910 Ser Ser Thr Phe Asp Ala Gly Ala Gly Ile Ala Leu Asn Asp His Phe 290 295 300 GTC AAG CTC ATT TCC TGG TAT GAC AAC GAA TTT GGC TAC AGC AAC AGG 958 Val Lys Leu Ile Ser Trp Tyr Asp Asn Glu Phe Gly Tyr Ser Asn Arg 305 310 315 GTG GTG GAC CTC ATG GCC CAC ATG CTATAGTGAG TCGTATT 999 Val Val Asp Leu Met Ala His Met 320 325 1049 base pairs nucleic acid single linear cDNA NO NO Homo sapiens CDS 1..372 experimental /partial /codon_start= 1 /function= “tumor suppressor” /product= “p53 (C-terminal portion)” /evidence= EXPERIMENTAL /gene= “HSP53G” /standard_name= “p53” 3′UTR 373..1049 /citation= ([1]) P. A. Barrett, J. C. Wiseman, R. W.Futreal An Alu polymorphism intragenic to the TP53 gene Nucleic Acids Res. 19 24 6977- 1991 39 FROM 1 TO 1049 39 GAG GTG CGT GTT TGT GCC TGT CCT GGG AGA GAC CGG CGC ACA GAG GAA 48 Glu Val Arg Val Cys Ala Cys Pro Gly Arg Asp Arg Arg Thr Glu Glu 1 5 10 15 GAG AAT CTC CGC AAG AAA GGG GAG CCT CAC CAC GAG CTG CCC CCA GGG 96 Glu Asn Leu Arg Lys Lys Gly Glu Pro His His Glu Leu Pro Pro Gly 20 25 30 AGC ACT AAG CGA GCA CTG CCC AAC AAC ACC AGC TCC TCT CCC CAG CCA 144 Ser Thr Lys Arg Ala Leu Pro Asn Asn Thr Ser Ser Ser Pro Gln Pro 35 40 45 AAG AAG AAA CCA CTG GAT GGA GAA TAT TTC ACC CTT CAG ATC CGT GGG 192 Lys Lys Lys Pro Leu Asp Gly Glu Tyr Phe Thr Leu Gln Ile Arg Gly 50 55 60 CGT GAG CGC TTC GAG ATG TTC CGA GAG CTG AAT GAG GCC TTG GAA CTC 240 Arg Glu Arg Phe Glu Met Phe Arg Glu Leu Asn Glu Ala Leu Glu Leu 65 70 75 80 AAG GAT GCC CAG GCT GGG AAG GAG CCA GGG GGG AGC AGG GCT CAC TCC 288 Lys Asp Ala Gln Ala Gly Lys Glu Pro Gly Gly Ser Arg Ala His Ser 85 90 95 AGC CAC CTG AAG TCC AAA AAG GGT CAG TCT ACC TCC CGC CAT AAA AAA 336 Ser His Leu Lys Ser Lys Lys Gly Gln Ser Thr Ser Arg His Lys Lys 100 105 110 CTC ATG TTC AAG ACA GAA GGG CCT GAC TCA GAC TGA CATTCTCCAC 382 Leu Met Phe Lys Thr Glu Gly Pro Asp Ser Asp * 115 120 TTCTTGTTCC CCACTGACAG CCTCCCTCCC CCATCTCTCC CTCCCCTGCC ATTTTGGGTT 442 TTGGGTCTTT GAACCCTTGC TTGCAATAGG TGTGCGTCAG AAGCACCCAG GACTTCCATT 502 TGCTTTGTCC CGGGGCTCCA CTGAACAAGT TGGCCTGCAC TGGTGTTTTG TTGTGGGGAG 562 GAGGATGGGG AGTAGGACAT ACCAGCTTAG ATTTTAAGGT TTTTACTGTG AGGGATGTTT 622 GGGAGATGTA AGAAATGTTC TTGCAGTTAA GGGTTAGTTT ACAATCAGCC ACATTCTAGG 682 TAGGTAGGGG CCCACTTCAC CGTACTAACC AGGGAAGCTG TCCCTCATGT TGAATTTTCT 742 CTAACTTCAA GGCCCATATC TGTGAAATGC TGGCATTTGC ACCTACCTCA CAGAGTGCAT 802 TGTGAGGGTT AATGAAATAA TGTACATCTG GCCTTGAAAC CACCTTTTAT TACATGGGGT 862 CTAAAACTTG ACCCCCTTGA GGGTGCCTGT TCCCTCTCCC TCTCCCTGTT GGCTGGTGGG 922 TTGGTAGTTT CTACAGTTGG GCAGCTGGTT AGGTAGAGGG AGTTGTCAAG TCTTGCTGGC 982 CCAGCCAAAC CCTGTCTGAC AACCTCTTGG TCGACCTTAG TACCTAAAAG GAAATCTCAC 1042 CCCATCC 1049 17 base pairs nucleic acid single linear cDNA NO NO not provided 40 TTCTTCCACA TTCACCT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 41 TCTTCCACAT TCACCTT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 42 CTTCCACATT CACCTTG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 43 TTCCACATTC ACCTTGC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 44 TCCACATTCA CCTTGCC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 45 CCACATTCAC CTTGCCC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 46 CACATTCACC TTGCCCC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 47 ACATTCACCT TGCCCCA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 48 CATTCACCTT GCCCCAC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 49 ATTCACCTTG CCCCACA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 50 TTCACCTTGC CCCACAG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 51 TCACCTTGCC CCACAGG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 52 CACCTTGCCC CACAGGG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 53 ACCTTGCCCC ACAGGGC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 54 CCTTGCCCCA CAGGGCA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 55 CTTGCCCCAC AGGGCAG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 56 TTGCCCCACA GGGCAGT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 57 TGCCCCACAG GGCAGTG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 58 GCCCCACAGG GCAGTGA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 59 CCCCACAGGG CAGTGAC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 60 CCCACAGGGC AGTGACC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 61 CCACAGGGCA GTGACCG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 62 CACAGGGCAG TGACCGC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 63 ACAGGGCAGT GACCGCA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 64 CAGGGCAGTG ACCGCAG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 65 AGGGCAGTGA CCGCAGA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 66 GGGCAGTGAC CGCAGAC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 67 GGCAGTGACC GCAGACT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 68 GCAGTGACCG CAGACTT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 69 CAGTGACCGC AGACTTC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 70 AGTGACCGCA GACTTCT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 71 GTGACCGCAG ACTTCTC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 72 TGACCGCAGA CTTCTCC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 73 GACCGCAGAC TTCTCCT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 74 ACCGCAGACT TCTCCTC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 75 CCGCAGACTT CTCCTCA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 76 CGCAGACTTC TCCTCAC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 77 GCAGACTTCT CCTCACT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 78 CAGACTTCTC CTCACTG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 79 AGACTTCTCC TCACTGG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 80 GACTTCTCCT CACTGGA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 81 ACTTCTCCTC ACTGGAC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 82 CTTCTCCTCA CTGGACA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 83 TTCTCCTCAC TGGACAG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 84 TCTCCTCACT GGACAGA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 85 CTCCTCACTG GACAGAT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 86 TCCTCACTGG ACAGATG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 87 CCTCACTGGA CAGATGC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 88 CTCACTGGAC AGATGCA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 89 TCACTGGACA GATGCAC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 90 CACTGGACAG ATGCACC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 91 ACTGGACAGA TGCACCA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 92 CTGGACAGAT GCACCAT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 93 TGGACAGATG CACCATT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 94 GGACAGATGC ACCATTC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 95 GACAGATGCA CCATTCT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 96 ACAGATGCAC CATTCTG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 97 CAGATGCACC ATTCTGT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 98 AGATGCACCA TTCTGTC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 99 GATGCACCAT TCTGTCT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 100 ATGCACCATT CTGTCTG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 101 TGCACCATTC TGTCTGT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 102 GCACCATTCT GTCTGTT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 103 CACCATTCTG TCTGTTT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 104 ACCATTCTGT CTGTTTT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 105 CCATTCTGTC TGTTTTG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 106 CATTCTGTCT GTTTTGG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 107 ATTCTGTCTG TTTTGGG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 108 TTCTGTCTGT TTTGGGG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 109 TCTGTCTGTT TTGGGGG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 110 CTGTCTGTTT TGGGGGA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 111 TGTCTGTTTT GGGGGAT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 112 GTCTGTTTTG GGGGATT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 113 TCTGTTTTGG GGGATTG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 114 CTGTTTTGGG GGATTGC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 115 TGTTTTGGGG GATTGCA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 116 GTTTTGGGGG ATTGCAA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 117 TTTTGGGGGA TTGCAAG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 118 TTTGGGGGAT TGCAAGT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 119 TTGGGGGATT GCAAGTA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 120 TGGGGGATTG CAAGTAA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 121 GGGGGATTGC AAGTAAA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 122 GGGGATTGCA AGTAAAC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 123 GGGATTGCAA GTAAACA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 124 GGATTGCAAG TAAACAC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 125 GATTGCAAGT AAACACA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 126 ATTGCAAGTA AACACAG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 127 TTGCAAGTAA ACACAGT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 128 TGCAAGTAAA CACAGTT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 129 GCAAGTAAAC ACAGTTG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 130 CAAGTAAACA CAGTTGT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 131 AAGTAAACAC AGTTGTG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 132 AGTAAACACA GTTGTGT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 133 GTAAACACAG TTGTGTC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 134 TAAACACAGT TGTGTCA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 135 AAACACAGTT GTGTCAA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 136 AACACAGTTG TGTCAAA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 137 ACACAGTTGT GTCAAAA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 138 CACAGTTGTG TCAAAAG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 139 ACAGTTGTGT CAAAAGC 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 140 CAGTTGTGTC AAAAGCA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 141 AGTTGTGTCA AAAGCAA 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 142 GTTGTGTCAA AAGCAAG 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 143 TTGTGTCAAA AGCAAGT 17 17 base pairs nucleic acid single linear cDNA NO NO not provided 144 TGTGTCAAAA GCAAGTG 17 20 base pairs nucleic acid single linear cDNA NO NO not provided 145 GTACTGTCCA TTTATCAGGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 146 TACTGTCCAT TTATCAGGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 147 ACTGTCCATT TATCAGGATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 148 CTGTCCATTT ATCAGGATGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 149 TGTCCATTTA TCAGGATGGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 150 GTCCATTTAT CAGGATGGAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 151 TCCATTTATC AGGATGGAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 152 CCATTTATCA GGATGGAGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 153 CATTTATCAG GATGGAGTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 154 ATTTATCAGG ATGGAGTTCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 155 TTTATCAGGA TGGAGTTCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 156 TTATCAGGAT GGAGTTCATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 157 TATCAGGATG GAGTTCATAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 158 ATCAGGATGG AGTTCATAAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 159 TCAGGATGGA GTTCATAACC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 160 CAGGATGGAG TTCATAACCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 161 AGGATGGAGT TCATAACCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 162 GGATGGAGTT CATAACCCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 163 GATGGAGTTC ATAACCCATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 164 ATGGAGTTCA TAACCCATCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 165 TGGAGTTCAT AACCCATCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 166 GGAGTTCATA ACCCATCCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 167 GAGTTCATAA CCCATCCCAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 168 AGTTCATAAC CCATCCCAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 169 GTTCATAACC CATCCCAAAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 170 TTCATAACCC ATCCCAAAGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 171 TCATAACCCA TCCCAAAGGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 172 CATAACCCAT CCCAAAGGAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 173 ATAACCCATC CCAAAGGAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 174 TAACCCATCC CAAAGGAATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 175 AACCCATCCC AAAGGAATGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 176 ACCCATCCCA AAGGAATGGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 177 CCCATCCCAA AGGAATGGAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 178 CCATCCCAAA GGAATGGAGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 179 CATCCCAAAG GAATGGAGGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 180 ATCCCAAAGG AATGGAGGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 181 TCCCAAAGGA ATGGAGGTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 182 CCCAAAGGAA TGGAGGTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 183 CCAAAGGAAT GGAGGTTCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 184 CAAAGGAATG GAGGTTCTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 185 AAAGGAATGG AGGTTCTTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 186 AAGGAATGGA GGTTCTTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 187 AGGAATGGAG GTTCTTTCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 188 GGAATGGAGG TTCTTTCTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 189 GAATGGAGGT TCTTTCTGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 190 AATGGAGGTT CTTTCTGATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 191 ATGGAGGTTC TTTCTGATGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 192 TGGAGGTTCT TTCTGATGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 193 GGAGGTTCTT TCTGATGTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 194 GAGGTTCTTT CTGATGTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 195 AGGTTCTTTC TGATGTTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 196 GGTTCTTTCT GATGTTTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 197 GTTCTTTCTG ATGTTTTTTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 198 TTCTTTCTGA TGTTTTTTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 199 TCTTTCTGAT GTTTTTTGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 200 CTTTCTGATG TTTTTTGTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 201 TTTCTGATGT TTTTTGTCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 202 TTCTGATGTT TTTTGTCTGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 203 TCTGATGTTT TTTGTCTGGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 204 CTGATGTTTT TTGTCTGGTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 205 TGATGTTTTT TGTCTGGTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 206 GATGTTTTTT GTCTGGTGTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 207 ATGTTTTTTG TCTGGTGTGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 208 TGTTTTTTGT CTGGTGTGGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 209 GTTTTTTGTC TGGTGTGGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 210 TTTTTTGTCT GGTGTGGTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 211 TTTTTGTCTG GTGTGGTAAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 212 TTTTGTCTGG TGTGGTAAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 213 TTTGTCTGGT GTGGTAAGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 214 TTGTCTGGTG TGGTAAGTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 215 TGTCTGGTGT GGTAAGTCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 216 GTCTGGTGTG GTAAGTCCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 217 TCTGGTGTGG TAAGTCCCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 218 CTGGTGTGGT AAGTCCCCAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 219 TGGTGTGGTA AGTCCCCACC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 220 GGTGTGGTAA GTCCCCACCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 221 GTGTGGTAAG TCCCCACCTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 222 TGTGGTAAGT CCCCACCTCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 223 GTGGTAAGTC CCCACCTCAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 224 TGGTAAGTCC CCACCTCAAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 225 GGTAAGTCCC CACCTCAACA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 226 GTAAGTCCCC ACCTCAACAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 227 TAAGTCCCCA CCTCAACAGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 228 AAGTCCCCAC CTCAACAGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 229 AGTCCCCACC TCAACAGATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 230 GTCCCCACCT CAACAGATGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 231 TCCCCACCTC AACAGATGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 232 CCCCACCTCA ACAGATGTTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 233 CCCACCTCAA CAGATGTTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 234 CCACCTCAAC AGATGTTGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 235 CACCTCAACA GATGTTGTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 236 ACCTCAACAG ATGTTGTCTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 237 CCTCAACAGA TGTTGTCTCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 238 CTCAACAGAT GTTGTCTCAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 239 TCAACAGATG TTGTCTCAGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 240 CAACAGATGT TGTCTCAGCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 241 AACAGATGTT GTCTCAGCTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 242 ACAGATGTTG TCTCAGCTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 243 CAGATGTTGT CTCAGCTCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 244 AGATGTTGTC TCAGCTCCTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 245 GATGTTGTCT CAGCTCCTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 246 ATGTTGTCTC AGCTCCTCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 247 TGTTGTCTCA GCTCCTCTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 248 GTTGTCTCAG CTCCTCTATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 249 TTGTCTCAGC TCCTCTATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 250 TGTCTCAGCT CCTCTATTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 251 GTCTCAGCTC CTCTATTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 252 TCTCAGCTCC TCTATTTTTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 253 CTCAGCTCCT CTATTTTTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 254 TCAGCTCCTC TATTTTTGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 255 CAGCTCCTCT ATTTTTGTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 256 AGCTCCTCTA TTTTTGTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 257 GCTCCTCTAT TTTTGTTCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 258 CTCCTCTATT TTTGTTCTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 259 TCCTCTATTT TTGTTCTATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 260 CCTCTATTTT TGTTCTATGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 261 CTCTATTTTT GTTCTATGCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 262 TCTATTTTTG TTCTATGCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 263 CTATTTTTGT TCTATGCTGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 264 TATTTTTGTT CTATGCTGCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 265 ATTTTTGTTC TATGCTGCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 266 TTTTTGTTCT ATGCTGCCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 267 TTTTGTTCTA TGCTGCCCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 268 TTTGTTCTAT GCTGCCCTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 269 TTGTTCTATG CTGCCCTATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 270 TGTTCTATGC TGCCCTATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 271 GTTCTATGCT GCCCTATTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 272 TTCTATGCTG CCCTATTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 273 TCTATGCTGC CCTATTTCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 274 CTATGCTGCC CTATTTCTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 275 TATGCTGCCC TATTTCTAAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 276 ATGCTGCCCT ATTTCTAAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 277 TGCTGCCCTA TTTCTAAGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 278 GCTGCCCTAT TTCTAAGTCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 279 CTGCCCTATT TCTAAGTCAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 280 TGCCCTATTT CTAAGTCAGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 281 GCCCTATTTC TAAGTCAGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 282 CCCTATTTCT AAGTCAGATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 283 CCTATTTCTA AGTCAGATCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 284 CTATTTCTAA GTCAGATCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 285 TATTTCTAAG TCAGATCCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 286 ATTTCTAAGT CAGATCCTAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 287 TTTCTAAGTC AGATCCTACA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 288 TTCTAAGTCA GATCCTACAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 289 TCTAAGTCAG ATCCTACATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 290 CTAAGTCAGA TCCTACATAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 291 TAAGTCAGAT CCTACATACA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 292 AAGTCAGATC CTACATACAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 293 AGTCAGATCC TACATACAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 294 GTCAGATCCT ACATACAAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 295 TCAGATCCTA CATACAAATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 296 CAGATCCTAC ATACAAATCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 297 AGATCCTACA TACAAATCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 298 GATCCTACAT ACAAATCATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 299 ATCCTACATA CAAATCATCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 300 TCCTACATAC AAATCATCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 301 CCTACATACA AATCATCCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 302 CTACATACAA ATCATCCATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 303 TACATACAAA TCATCCATGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 304 ACATACAAAT CATCCATGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 305 CATACAAATC ATCCATGTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 306 ATACAAATCA TCCATGTATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 307 TACAAATCAT CCATGTATTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 308 ACAAATCATC CATGTATTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 309 CAAATCATCC ATGTATTGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 310 AAATCATCCA TGTATTGATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 311 AATCATCCAT GTATTGATAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 312 ATCATCCATG TATTGATAGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 313 TCATCCATGT ATTGATAGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 314 CATCCATGTA TTGATAGATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 315 ATCCATGTAT TGATAGATAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 316 TCCATGTATT GATAGATAAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 317 CCATGTATTG ATAGATAACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 318 CATGTATTGA TAGATAACTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 319 ATGTATTGAT AGATAACTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 320 TGTATTGATA GATAACTATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 321 GTATTGATAG ATAACTATGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 322 TATTGATAGA TAACTATGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 323 ATTGATAGAT AACTATGTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 324 TTGATAGATA ACTATGTCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 325 TGATAGATAA CTATGTCTGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 326 GATAGATAAC TATGTCTGGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 327 ATAGATAACT ATGTCTGGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 328 TAGATAACTA TGTCTGGATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 329 AGATAACTAT GTCTGGATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 330 GATAACTATG TCTGGATTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 331 ATAACTATGT CTGGATTTTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 332 TAACTATGTC TGGATTTTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 333 AACTATGTCT GGATTTTGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 334 ACTATGTCTG GATTTTGTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 335 CTATGTCTGG ATTTTGTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 336 TATGTCTGGA TTTTGTTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 337 ATGTCTGGAT TTTGTTTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 338 TGTCTGGATT TTGTTTTTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 339 GTCTGGATTT TGTTTTTTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 340 TCTGGATTTT GTTTTTTAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 341 CTGGATTTTG TTTTTTAAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 342 TGGATTTTGT TTTTTAAAAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 343 GGATTTTGTT TTTTAAAAGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 344 GATTTTGTTT TTTAAAAGGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 345 ATTTTGTTTT TTAAAAGGCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 346 TTTTGTTTTT TAAAAGGCTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 347 TTTGTTTTTT AAAAGGCTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 348 TTGTTTTTTA AAAGGCTCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 349 TGTTTTTTAA AAGGCTCTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 350 GTTTTTTAAA AGGCTCTAAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 351 TTTTTTAAAA GGCTCTAAGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 352 TTTTTAAAAG GCTCTAAGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 353 TTTTAAAAGG CTCTAAGATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 354 TTTAAAAGGC TCTAAGATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 355 TTAAAAGGCT CTAAGATTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 356 TAAAAGGCTC TAAGATTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 357 AAAAGGCTCT AAGATTTTTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 358 AAAGGCTCTA AGATTTTTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 359 AAGGCTCTAA GATTTTTGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 360 AGGCTCTAAG ATTTTTGTCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 361 GGCTCTAAGA TTTTTGTCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 362 GCTCTAAGAT TTTTGTCATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 363 CTCTAAGATT TTTGTCATGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 364 TCTAAGATTT TTGTCATGCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 365 CTAAGATTTT TGTCATGCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 366 TAAGATTTTT GTCATGCTAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 367 AAGATTTTTG TCATGCTACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 368 AGATTTTTGT CATGCTACTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 369 GATTTTTGTC ATGCTACTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 370 ATTTTTGTCA TGCTACTTTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 371 TTTTTGTCAT GCTACTTTGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 372 TTTTGTCATG CTACTTTGGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 373 TTTGTCATGC TACTTTGGAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 374 TTGTCATGCT ACTTTGGAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 375 TGTCATGCTA CTTTGGAATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 376 GTCATGCTAC TTTGGAATAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 377 TCATGCTACT TTGGAATATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 378 CATGCTACTT TGGAATATTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 379 ATGCTACTTT GGAATATTGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 380 TGCTACTTTG GAATATTGCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 381 GCTACTTTGG AATATTGCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 382 CTACTTTGGA ATATTGCTGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 383 TACTTTGGAA TATTGCTGGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 384 ACTTTGGAAT ATTGCTGGTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 385 CTTTGGAATA TTGCTGGTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 386 TTTGGAATAT TGCTGGTGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 387 TTGGAATATT GCTGGTGATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 388 TGGAATATTG CTGGTGATCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 389 GGAATATTGC TGGTGATCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 390 GAATATTGCT GGTGATCCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 391 AATATTGCTG GTGATCCTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 392 ATATTGCTGG TGATCCTTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 393 TATTGCTGGT GATCCTTTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 394 ATTGCTGGTG ATCCTTTCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 395 TTGCTGGTGA TCCTTTCCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 396 TGCTGGTGAT CCTTTCCATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 397 GCTGGTGATC CTTTCCATCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 398 CTGGTGATCC TTTCCATCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 399 TGGTGATCCT TTCCATCCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 400 GGTGATCCTT TCCATCCCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 401 GTGATCCTTT CCATCCCTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 402 TGATCCTTTC CATCCCTGTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 403 GATCCTTTCC ATCCCTGTGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 404 ATCCTTTCCA TCCCTGTGGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 405 TCCTTTCCAT CCCTGTGGAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 406 CCTTTCCATC CCTGTGGAAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 407 CTTTCCATCC CTGTGGAAGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 408 TTTCCATCCC TGTGGAAGCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 409 TTCCATCCCT GTGGAAGCAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 410 TCCATCCCTG TGGAAGCACA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 411 CCATCCCTGT GGAAGCACAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 412 CATCCCTGTG GAAGCACATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 413 ATCCCTGTGG AAGCACATTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 414 TCCCTGTGGA AGCACATTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 415 CCCTGTGGAA GCACATTGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 416 CCTGTGGAAG CACATTGTAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 417 CTGTGGAAGC ACATTGTACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 418 TGTGGAAGCA CATTGTACTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 419 GTGGAAGCAC ATTGTACTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 420 TGGAAGCACA TTGTACTGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 421 GGAAGCACAT TGTACTGATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 422 GAAGCACATT GTACTGATAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 423 AAGCACATTG TACTGATATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 424 AGCACATTGT ACTGATATCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 425 GCACATTGTA CTGATATCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 426 CACATTGTAC TGATATCTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 427 ACATTGTACT GATATCTAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 428 CATTGTACTG ATATCTAATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 429 ATTGTACTGA TATCTAATCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 430 TTGTACTGAT ATCTAATCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 431 TGTACTGATA TCTAATCCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 432 GTACTGATAT CTAATCCCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 433 TACTGATATC TAATCCCTGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 434 ACTGATATCT AATCCCTGGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 435 CTGATATCTA ATCCCTGGTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 436 TGATATCTAA TCCCTGGTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 437 GATATCTAAT CCCTGGTGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 438 ATATCTAATC CCTGGTGTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 439 TATCTAATCC CTGGTGTCTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 440 ATCTAATCCC TGGTGTCTCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 441 TCTAATCCCT GGTGTCTCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 442 CTAATCCCTG GTGTCTCATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 443 TAATCCCTGG TGTCTCATTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 444 AATCCCTGGT GTCTCATTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 445 ATCCCTGGTG TCTCATTGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 446 TCCCTGGTGT CTCATTGTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 447 CCCTGGTGTC TCATTGTTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 448 CCTGGTGTCT CATTGTTTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 449 CTGGTGTCTC ATTGTTTATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 450 TGGTGTCTCA TTGTTTATAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 451 GGTGTCTCAT TGTTTATACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 452 GTGTCTCATT GTTTATACTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 453 TGTCTCATTG TTTATACTAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 454 GTCTCATTGT TTATACTAGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 455 TCTCATTGTT TATACTAGGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 456 CTCATTGTTT ATACTAGGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 457 TCATTGTTTA TACTAGGTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 458 CATTGTTTAT ACTAGGTATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 459 ATTGTTTATA CTAGGTATGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 460 TTGTTTATAC TAGGTATGGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 461 TGTTTATACT AGGTATGGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 462 GTTTATACTA GGTATGGTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 463 TTTATACTAG GTATGGTAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 464 TTATACTAGG TATGGTAAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 465 TATACTAGGT ATGGTAAATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 466 ATACTAGGTA TGGTAAATGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 467 TACTAGGTAT GGTAAATGCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 468 ACTAGGTATG GTAAATGCAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 469 CTAGGTATGG TAAATGCAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 470 TAGGTATGGT AAATGCAGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 471 AGGTATGGTA AATGCAGTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 472 GGTATGGTAA ATGCAGTATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 473 GTATGGTAAA TGCAGTATAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 474 TATGGTAAAT GCAGTATACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 475 ATGGTAAATG CAGTATACTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 476 TGGTAAATGC AGTATACTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 477 GGTAAATGCA GTATACTTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 478 GTAAATGCAG TATACTTCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 479 TAAATGCAGT ATACTTCCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 480 AAATGCAGTA TACTTCCTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 481 AATGCAGTAT ACTTCCTGAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 482 ATGCAGTATA CTTCCTGAAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 483 TGCAGTATAC TTCCTGAAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 484 GCAGTATACT TCCTGAAGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 485 CAGTATACTT CCTGAAGTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 486 AGTATACTTC CTGAAGTCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 487 GTATACTTCC TGAAGTCTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 488 TATACTTCCT GAAGTCTTCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 489 ATACTTCCTG AAGTCTTCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 490 TACTTCCTGA AGTCTTCATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 491 ACTTCCTGAA GTCTTCATCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 492 CTTCCTGAAG TCTTCATCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 493 TTCCTGAAGT CTTCATCTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 494 TCCTGAAGTC TTCATCTAAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 495 CCTGAAGTCT TCATCTAAGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 496 CTGAAGTCTT CATCTAAGGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 497 TGAAGTCTTC ATCTAAGGGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 498 GAAGTCTTCA TCTAAGGGAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 499 AAGTCTTCAT CTAAGGGAAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 500 AGTCTTCATC TAAGGGAACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 501 GTCTTCATCT AAGGGAACTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 502 TCTTCATCTA AGGGAACTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 503 CTTCATCTAA GGGAACTGAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 504 TTCATCTAAG GGAACTGAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 505 TCATCTAAGG GAACTGAAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 506 CATCTAAGGG AACTGAAAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 507 ATCTAAGGGA ACTGAAAAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 508 TCTAAGGGAA CTGAAAAATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 509 CTAAGGGAAC TGAAAAATAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 510 TAAGGGAACT GAAAAATATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 511 AAGGGAACTG AAAAATATGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 512 AGGGAACTGA AAAATATGCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 513 GGGAACTGAA AAATATGCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 514 GGAACTGAAA AATATGCATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 515 GAACTGAAAA ATATGCATCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 516 AACTGAAAAA TATGCATCAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 517 ACTGAAAAAT ATGCATCACC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 518 CTGAAAAATA TGCATCACCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 519 TGAAAAATAT GCATCACCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 520 GAAAAATATG CATCACCCAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 521 AAAAATATGC ATCACCCACA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 522 AAAATATGCA TCACCCACAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 523 AAATATGCAT CACCCACATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 524 AATATGCATC ACCCACATCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 525 ATATGCATCA CCCACATCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 526 TATGCATCAC CCACATCCAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 527 ATGCATCACC CACATCCAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 528 TGCATCACCC ACATCCAGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 529 GCATCACCCA CATCCAGTAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 530 CATCACCCAC ATCCAGTACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 531 ATCACCCACA TCCAGTACTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 532 TCACCCACAT CCAGTACTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 533 CACCCACATC CAGTACTGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 534 ACCCACATCC AGTACTGTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 535 CCCACATCCA GTACTGTTAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 536 CCACATCCAG TACTGTTACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 537 CACATCCAGT ACTGTTACTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 538 ACATCCAGTA CTGTTACTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 539 CATCCAGTAC TGTTACTGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 540 ATCCAGTACT GTTACTGATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 541 TCCAGTACTG TTACTGATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 542 CCAGTACTGT TACTGATTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 543 CAGTACTGTT ACTGATTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 544 AGTACTGTTA CTGATTTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 545 GTACTGTTAC TGATTTTTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 546 TACTGTTACT GATTTTTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 547 ACTGTTACTG ATTTTTTCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 548 CTGTTACTGA TTTTTTCTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 549 TGTTACTGAT TTTTTCTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 550 GTTACTGATT TTTTCTTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 551 TTACTGATTT TTTCTTTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 552 TACTGATTTT TTCTTTTTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 553 ACTGATTTTT TCTTTTTTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 554 CTGATTTTTT CTTTTTTAAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 555 TGATTTTTTC TTTTTTAACC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 556 GATTTTTTCT TTTTTAACCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 557 ATTTTTTCTT TTTTAACCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 558 TTTTTTCTTT TTTAACCCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 559 TTTTTCTTTT TTAACCCTGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 560 TTTTCTTTTT TAACCCTGCG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 561 TTTCTTTTTT AACCCTGCGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 562 TTCTTTTTTA ACCCTGCGGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 563 TCTTTTTTAA CCCTGCGGGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 564 CTTTTTTAAC CCTGCGGGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 565 TTTTTTAACC CTGCGGGATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 566 TTTTTAACCC TGCGGGATGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 567 TTTTAACCCT GCGGGATGTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 568 TTTAACCCTG CGGGATGTGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 569 TTAACCCTGC GGGATGTGGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 570 TAACCCTGCG GGATGTGGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 571 AACCCTGCGG GATGTGGTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 572 ACCCTGCGGG ATGTGGTATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 573 CCCTGCGGGA TGTGGTATTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 574 CCTGCGGGAT GTGGTATTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 575 CTGCGGGATG TGGTATTCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 576 TGCGGGATGT GGTATTCCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 577 GCGGGATGTG GTATTCCTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 578 CGGGATGTGG TATTCCTAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 579 GGGATGTGGT ATTCCTAATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 580 GGATGTGGTA TTCCTAATTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 581 GATGTGGTAT TCCTAATTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 582 ATGTGGTATT CCTAATTGAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 583 TGTGGTATTC CTAATTGAAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 584 GTGGTATTCC TAATTGAACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 585 TGGTATTCCT AATTGAACTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 586 GGTATTCCTA ATTGAACTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 587 GTATTCCTAA TTGAACTTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 588 TATTCCTAAT TGAACTTCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 589 ATTCCTAATT GAACTTCCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 590 TTCCTAATTG AACTTCCCAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 591 TCCTAATTGA ACTTCCCAGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 592 CCTAATTGAA CTTCCCAGAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 593 CTAATTGAAC TTCCCAGAAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 594 TAATTGAACT TCCCAGAAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 595 AATTGAACTT CCCAGAAGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 596 ATTGAACTTC CCAGAAGTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 597 TTGAACTTCC CAGAAGTCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 598 TGAACTTCCC AGAAGTCTTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 599 GAACTTCCCA GAAGTCTTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 600 AACTTCCCAG AAGTCTTGAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 601 ACTTCCCAGA AGTCTTGAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 602 CTTCCCAGAA GTCTTGAGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 603 TTCCCAGAAG TCTTGAGTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 604 TCCCAGAAGT CTTGAGTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 605 CCCAGAAGTC TTGAGTTCTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 606 CCAGAAGTCT TGAGTTCTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 607 CAGAAGTCTT GAGTTCTCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 608 AGAAGTCTTG AGTTCTCTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 609 GAAGTCTTGA GTTCTCTTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 610 AAGTCTTGAG TTCTCTTATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 611 AGTCTTGAGT TCTCTTATTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 612 GTCTTGAGTT CTCTTATTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 613 TCTTGAGTTC TCTTATTAAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 614 CTTGAGTTCT CTTATTAAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 615 TTGAGTTCTC TTATTAAGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 616 TGAGTTCTCT TATTAAGTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 617 GAGTTCTCTT ATTAAGTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 618 AGTTCTCTTA TTAAGTTCTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 619 GTTCTCTTAT TAAGTTCTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 620 TTCTCTTATT AAGTTCTCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 621 TCTCTTATTA AGTTCTCTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 622 CTCTTATTAA GTTCTCTGAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 623 TCTTATTAAG TTCTCTGAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 624 CTTATTAAGT TCTCTGAAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 625 TTATTAAGTT CTCTGAAATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 626 TATTAAGTTC TCTGAAATCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 627 ATTAAGTTCT CTGAAATCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 628 TTAAGTTCTC TGAAATCTAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 629 TAAGTTCTCT GAAATCTACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 630 AAGTTCTCTG AAATCTACTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 631 AGTTCTCTGA AATCTACTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 632 GTTCTCTGAA ATCTACTAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 633 TTCTCTGAAA TCTACTAATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 634 TCTCTGAAAT CTACTAATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 635 CTCTGAAATC TACTAATTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 636 TCTGAAATCT ACTAATTTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 637 CTGAAATCTA CTAATTTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 638 TGAAATCTAC TAATTTTCTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 639 GAAATCTACT AATTTTCTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 640 AAATCTACTA ATTTTCTCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 641 AATCTACTAA TTTTCTCCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 642 ATCTACTAAT TTTCTCCATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 643 TCTACTAATT TTCTCCATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 644 CTACTAATTT TCTCCATTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 645 TACTAATTTT CTCCATTTAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 646 ACTAATTTTC TCCATTTAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 647 CTAATTTTCT CCATTTAGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 648 TAATTTTCTC CATTTAGTAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 649 AATTTTCTCC ATTTAGTACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 650 ATTTTCTCCA TTTAGTACTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 651 TTTTCTCCAT TTAGTACTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 652 TTTCTCCATT TAGTACTGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 653 TTCTCCATTT AGTACTGTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 654 TCTCCATTTA GTACTGTCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 655 CTCCATTTAG TACTGTCTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 656 TCCATTTAGT ACTGTCTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 657 CCATTTAGTA CTGTCTTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 658 CATTTAGTAC TGTCTTTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 659 ATTTAGTACT GTCTTTTTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 660 TTTAGTACTG TCTTTTTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 661 TTAGTACTGT CTTTTTTCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 662 TAGTACTGTC TTTTTTCTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 663 AGTACTGTCT TTTTTCTTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 664 GTACTGTCTT TTTTCTTTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 665 TACTGTCTTT TTTCTTTATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 666 ACTGTCTTTT TTCTTTATGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 667 CTGTCTTTTT TCTTTATGGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 668 TGTCTTTTTT CTTTATGGCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 669 GTCTTTTTTC TTTATGGCAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 670 TCTTTTTTCT TTATGGCAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 671 CTTTTTTCTT TATGGCAAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 672 TTTTTTCTTT ATGGCAAATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 673 TTTTTCTTTA TGGCAAATAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 674 TTTTCTTTAT GGCAAATACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 675 TTTCTTTATG GCAAATACTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 676 TTCTTTATGG CAAATACTGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 677 TCTTTATGGC AAATACTGGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 678 CTTTATGGCA AATACTGGAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 679 TTTATGGCAA ATACTGGAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 680 TTATGGCAAA TACTGGAGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 681 TATGGCAAAT ACTGGAGTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 682 ATGGCAAATA CTGGAGTATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 683 TGGCAAATAC TGGAGTATTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 684 GGCAAATACT GGAGTATTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 685 GCAAATACTG GAGTATTGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 686 CAAATACTGG AGTATTGTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 687 AAATACTGGA GTATTGTATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 688 AATACTGGAG TATTGTATGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 689 ATACTGGAGT ATTGTATGGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 690 TACTGGAGTA TTGTATGGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 691 ACTGGAGTAT TGTATGGATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 692 CTGGAGTATT GTATGGATTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 693 TGGAGTATTG TATGGATTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 694 GGAGTATTGT ATGGATTCTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 695 GAGTATTGTA TGGATTCTCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 696 AGTATTGTAT GGATTCTCAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 697 GTATTGTATG GATTCTCAGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 698 TATTGTATGG ATTCTCAGGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 699 ATTGTATGGA TTCTCAGGCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 700 TTGTATGGAT TCTCAGGCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 701 TGTATGGATT CTCAGGCCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 702 GTATGGATTC TCAGGCCCAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 703 TATGGATTCT CAGGCCCAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 704 ATGGATTCTC AGGCCCAATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 705 TGGATTCTCA GGCCCAATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 706 GGATTCTCAG GCCCAATTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 707 GATTCTCAGG CCCAATTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 708 ATTCTCAGGC CCAATTTTTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 709 TTCTCAGGCC CAATTTTTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 710 TCTCAGGCCC AATTTTTGAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 711 CTCAGGCCCA ATTTTTGAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 712 TCAGGCCCAA TTTTTGAAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 713 CAGGCCCAAT TTTTGAAATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 714 AGGCCCAATT TTTGAAATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 715 GGCCCAATTT TTGAAATTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 716 GCCCAATTTT TGAAATTTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 717 CCCAATTTTT GAAATTTTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 718 CCAATTTTTG AAATTTTCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 719 CAATTTTTGA AATTTTCCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 720 AATTTTTGAA ATTTTCCCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 721 ATTTTTGAAA TTTTCCCTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 722 TTTTTGAAAT TTTCCCTTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 723 TTTTGAAATT TTCCCTTCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 724 TTTGAAATTT TCCCTTCCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 725 TTGAAATTTT CCCTTCCTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 726 TGAAATTTTC CCTTCCTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 727 GAAATTTTCC CTTCCTTTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 728 AAATTTTCCC TTCCTTTTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 729 AATTTTCCCT TCCTTTTCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 730 ATTTTCCCTT CCTTTTCCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 731 TTTTCCCTTC CTTTTCCATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 732 TTTCCCTTCC TTTTCCATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 733 TTCCCTTCCT TTTCCATTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 734 TCCCTTCCTT TTCCATTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 735 CCCTTCCTTT TCCATTTCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 736 CCTTCCTTTT CCATTTCTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 737 CTTCCTTTTC CATTTCTGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 738 TTCCTTTTCC ATTTCTGTAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 739 TCCTTTTCCA TTTCTGTACA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 740 CCTTTTCCAT TTCTGTACAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 741 CTTTTCCATT TCTGTACAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 742 TTTTCCATTT CTGTACAAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 743 TTTCCATTTC TGTACAAATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 744 TTCCATTTCT GTACAAATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 745 TCCATTTCTG TACAAATTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 746 CCATTTCTGT ACAAATTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 747 CATTTCTGTA CAAATTTCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 748 ATTTCTGTAC AAATTTCTAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 749 TTTCTGTACA AATTTCTACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 750 TTCTGTACAA ATTTCTACTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 751 TCTGTACAAA TTTCTACTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 752 CTGTACAAAT TTCTACTAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 753 TGTACAAATT TCTACTAATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 754 GTACAAATTT CTACTAATGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 755 TACAAATTTC TACTAATGCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 756 ACAAATTTCT ACTAATGCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 757 CAAATTTCTA CTAATGCTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 758 AAATTTCTAC TAATGCTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 759 AATTTCTACT AATGCTTTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 760 ATTTCTACTA ATGCTTTTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 761 TTTCTACTAA TGCTTTTATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 762 TTCTACTAAT GCTTTTATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 763 TCTACTAATG CTTTTATTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 764 CTACTAATGC TTTTATTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 765 TACTAATGCT TTTATTTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 766 ACTAATGCTT TTATTTTTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 767 CTAATGCTTT TATTTTTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 768 TAATGCTTTT ATTTTTTCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 769 AATGCTTTTA TTTTTTCTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 770 ATGCTTTTAT TTTTTCTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 771 TGCTTTTATT TTTTCTTCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 772 GCTTTTATTT TTTCTTCTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 773 CTTTTATTTT TTCTTCTGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 774 TTTTATTTTT TCTTCTGTCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 775 TTTATTTTTT CTTCTGTCAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 776 TTATTTTTTC TTCTGTCAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 777 TATTTTTTCT TCTGTCAATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 778 ATTTTTTCTT CTGTCAATGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 779 TTTTTTCTTC TGTCAATGGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 780 TTTTTCTTCT GTCAATGGCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 781 TTTTCTTCTG TCAATGGCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 782 TTTCTTCTGT CAATGGCCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 783 TTCTTCTGTC AATGGCCATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 784 TCTTCTGTCA ATGGCCATTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 785 CTTCTGTCAA TGGCCATTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 786 TTCTGTCAAT GGCCATTGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 787 TCTGTCAATG GCCATTGTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 788 CTGTCAATGG CCATTGTTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 789 TGTCAATGGC CATTGTTTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 790 GTCAATGGCC ATTGTTTAAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 791 TCAATGGCCA TTGTTTAACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 792 CAATGGCCAT TGTTTAACTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 793 AATGGCCATT GTTTAACTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 794 ATGGCCATTG TTTAACTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 795 TGGCCATTGT TTAACTTTTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 796 GGCCATTGTT TAACTTTTGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 797 GCCATTGTTT AACTTTTGGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 798 CCATTGTTTA ACTTTTGGGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 799 CATTGTTTAA CTTTTGGGCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 800 ATTGTTTAAC TTTTGGGCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 801 TTGTTTAACT TTTGGGCCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 802 TGTTTAACTT TTGGGCCATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 803 GTTTAACTTT TGGGCCATCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 804 TTTAACTTTT GGGCCATCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 805 TTAACTTTTG GGCCATCCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 806 TAACTTTTGG GCCATCCATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 807 AACTTTTGGG CCATCCATTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 808 ACTTTTGGGC CATCCATTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 809 CTTTTGGGCC ATCCATTCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 810 TTTTGGGCCA TCCATTCCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 811 TTTGGGCCAT CCATTCCTGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 812 TTGGGCCATC CATTCCTGGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 813 TGGGCCATCC ATTCCTGGCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 814 GGGCCATCCA TTCCTGGCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 815 GGCCATCCAT TCCTGGCTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 816 GCCATCCATT CCTGGCTTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 817 CCATCCATTC CTGGCTTTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 818 CATCCATTCC TGGCTTTAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 819 ATCCATTCCT GGCTTTAATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 820 TCCATTCCTG GCTTTAATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 821 CCATTCCTGG CTTTAATTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 822 CATTCCTGGC TTTAATTTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 823 ATTCCTGGCT TTAATTTTAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 824 TTCCTGGCTT TAATTTTACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 825 TCCTGGCTTT AATTTTACTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 826 CCTGGCTTTA ATTTTACTGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 827 CTGGCTTTAA TTTTACTGGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 828 TGGCTTTAAT TTTACTGGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 829 GGCTTTAATT TTACTGGTAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 830 GCTTTAATTT TACTGGTACA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 831 CTTTAATTTT ACTGGTACAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 832 TTTAATTTTA CTGGTACAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 833 TTAATTTTAC TGGTACAGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 834 TAATTTTACT GGTACAGTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 835 AATTTTACTG GTACAGTCTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 836 ATTTTACTGG TACAGTCTCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 837 TTTTACTGGT ACAGTCTCAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 838 TTTACTGGTA CAGTCTCAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 839 TTACTGGTAC AGTCTCAATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 840 TACTGGTACA GTCTCAATAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 841 ACTGGTACAG TCTCAATAGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 842 CTGGTACAGT CTCAATAGGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 843 TGGTACAGTC TCAATAGGGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 844 GGTACAGTCT CAATAGGGCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 845 GTACAGTCTC AATAGGGCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 846 TACAGTCTCA ATAGGGCTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 847 ACAGTCTCAA TAGGGCTAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 848 CAGTCTCAAT AGGGCTAATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 849 AGTCTCAATA GGGCTAATGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 850 GTCTCAATAG GGCTAATGGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 851 TCTCAATAGG GCTAATGGGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 852 CTCAATAGGG CTAATGGGAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 853 TCAATAGGGC TAATGGGAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 854 CAATAGGGCT AATGGGAAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 855 AATAGGGCTA ATGGGAAAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 856 ATAGGGCTAA TGGGAAAATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 857 TAGGGCTAAT GGGAAAATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 858 AGGGCTAATG GGAAAATTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 859 GGGCTAATGG GAAAATTTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 860 GGCTAATGGG AAAATTTAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 861 GCTAATGGGA AAATTTAAAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 862 CTAATGGGAA AATTTAAAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 863 TAATGGGAAA ATTTAAAGTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 864 AATGGGAAAA TTTAAAGTGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 865 ATGGGAAAAT TTAAAGTGCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 866 TGGGAAAATT TAAAGTGCAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 867 GGGAAAATTT AAAGTGCAAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 868 GGAAAATTTA AAGTGCAACC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 869 GAAAATTTAA AGTGCAACCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 870 AAAATTTAAA GTGCAACCAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 871 AAATTTAAAG TGCAACCAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 872 AATTTAAAGT GCAACCAATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 873 ATTTAAAGTG CAACCAATCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 874 TTTAAAGTGC AACCAATCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 875 TTAAAGTGCA ACCAATCTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 876 TAAAGTGCAA CCAATCTGAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 877 AAAGTGCAAC CAATCTGAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 878 AAGTGCAACC AATCTGAGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 879 AGTGCAACCA ATCTGAGTCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 880 GTGCAACCAA TCTGAGTCAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 881 TGCAACCAAT CTGAGTCAAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 882 GCAACCAATC TGAGTCAACA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 883 CAACCAATCT GAGTCAACAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 884 AACCAATCTG AGTCAACAGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 885 ACCAATCTGA GTCAACAGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 886 CCAATCTGAG TCAACAGATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 887 CAATCTGAGT CAACAGATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 888 AATCTGAGTC AACAGATTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 889 ATCTGAGTCA ACAGATTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 890 TCTGAGTCAA CAGATTTCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 891 CTGAGTCAAC AGATTTCTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 892 TGAGTCAACA GATTTCTTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 893 GAGTCAACAG ATTTCTTCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 894 AGTCAACAGA TTTCTTCCAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 895 GTCAACAGAT TTCTTCCAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 896 TCAACAGATT TCTTCCAATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 897 CAACAGATTT CTTCCAATTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 898 AACAGATTTC TTCCAATTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 899 ACAGATTTCT TCCAATTATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 900 CAGATTTCTT CCAATTATGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 901 AGATTTCTTC CAATTATGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 902 GATTTCTTCC AATTATGTTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 903 ATTTCTTCCA ATTATGTTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 904 TTTCTTCCAA TTATGTTGAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 905 TTCTTCCAAT TATGTTGACA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 906 TCTTCCAATT ATGTTGACAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 907 CTTCCAATTA TGTTGACAGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 908 TTCCAATTAT GTTGACAGGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 909 TCCAATTATG TTGACAGGTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 910 CCAATTATGT TGACAGGTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 911 CAATTATGTT GACAGGTGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 912 AATTATGTTG ACAGGTGTAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 913 ATTATGTTGA CAGGTGTAGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 914 TTATGTTGAC AGGTGTAGGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 915 TATGTTGACA GGTGTAGGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 916 ATGTTGACAG GTGTAGGTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 917 TGTTGACAGG TGTAGGTCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 918 GTTGACAGGT GTAGGTCCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 919 TTGACAGGTG TAGGTCCTAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 920 TGACAGGTGT AGGTCCTACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 921 GACAGGTGTA GGTCCTACTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 922 ACAGGTGTAG GTCCTACTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 923 CAGGTGTAGG TCCTACTAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 924 AGGTGTAGGT CCTACTAATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 925 GGTGTAGGTC CTACTAATAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 926 GTGTAGGTCC TACTAATACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 927 TGTAGGTCCT ACTAATACTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 928 GTAGGTCCTA CTAATACTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 929 TAGGTCCTAC TAATACTGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 930 AGGTCCTACT AATACTGTAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 931 GGTCCTACTA ATACTGTACC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 932 GTCCTACTAA TACTGTACCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 933 TCCTACTAAT ACTGTACCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 934 CCTACTAATA CTGTACCTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 935 CTACTAATAC TGTACCTATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 936 TACTAATACT GTACCTATAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 937 ACTAATACTG TACCTATAGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 938 CTAATACTGT ACCTATAGCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 939 TAATACTGTA CCTATAGCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 940 AATACTGTAC CTATAGCTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 941 ATACTGTACC TATAGCTTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 942 TACTGTACCT ATAGCTTTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 943 ACTGTACCTA TAGCTTTATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 944 CTGTACCTAT AGCTTTATGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 945 TGTACCTATA GCTTTATGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 946 GTACCTATAG CTTTATGTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 947 TACCTATAGC TTTATGTCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 948 ACCTATAGCT TTATGTCCAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 949 CCTATAGCTT TATGTCCACA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 950 CTATAGCTTT ATGTCCACAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 951 TATAGCTTTA TGTCCACAGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 952 ATAGCTTTAT GTCCACAGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 953 TAGCTTTATG TCCACAGATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 954 AGCTTTATGT CCACAGATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 955 GCTTTATGTC CACAGATTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 956 CTTTATGTCC ACAGATTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 957 TTTATGTCCA CAGATTTCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 958 TTATGTCCAC AGATTTCTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 959 TATGTCCACA GATTTCTATG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 960 ATGTCCACAG ATTTCTATGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 961 TGTCCACAGA TTTCTATGAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 962 GTCCACAGAT TTCTATGAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 963 TCCACAGATT TCTATGAGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 964 CCACAGATTT CTATGAGTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 965 CACAGATTTC TATGAGTATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 966 ACAGATTTCT ATGAGTATCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 967 CAGATTTCTA TGAGTATCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 968 AGATTTCTAT GAGTATCTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 969 GATTTCTATG AGTATCTGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 970 ATTTCTATGA GTATCTGATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 971 TTTCTATGAG TATCTGATCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 972 TTCTATGAGT ATCTGATCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 973 TCTATGAGTA TCTGATCATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 974 CTATGAGTAT CTGATCATAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 975 TATGAGTATC TGATCATACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 976 ATGAGTATCT GATCATACTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 977 TGAGTATCTG ATCATACTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 978 GAGTATCTGA TCATACTGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 979 AGTATCTGAT CATACTGTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 980 GTATCTGATC ATACTGTCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 981 TATCTGATCA TACTGTCTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 982 ATCTGATCAT ACTGTCTTAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 983 TCTGATCATA CTGTCTTACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 984 CTGATCATAC TGTCTTACTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 985 TGATCATACT GTCTTACTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 986 GATCATACTG TCTTACTTTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 987 ATCATACTGT CTTACTTTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 988 TCATACTGTC TTACTTTGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 989 CATACTGTCT TACTTTGATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 990 ATACTGTCTT ACTTTGATAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 991 TACTGTCTTA CTTTGATAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 992 ACTGTCTTAC TTTGATAAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 993 CTGTCTTACT TTGATAAAAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 994 TGTCTTACTT TGATAAAACC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 995 GTCTTACTTT GATAAAACCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 996 TCTTACTTTG ATAAAACCTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 997 CTTACTTTGA TAAAACCTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 998 TTACTTTGAT AAAACCTCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 999 TACTTTGATA AAACCTCCAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1000 ACTTTGATAA AACCTCCAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1001 CTTTGATAAA ACCTCCAATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1002 TTTGATAAAA CCTCCAATTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1003 TTGATAAAAC CTCCAATTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1004 TGATAAAACC TCCAATTCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1005 GATAAAACCT CCAATTCCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1006 ATAAAACCTC CAATTCCCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1007 TAAAACCTCC AATTCCCCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1008 AAAACCTCCA ATTCCCCCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1009 AAACCTCCAA TTCCCCCTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1010 AACCTCCAAT TCCCCCTATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1011 ACCTCCAATT CCCCCTATCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1012 CCTCCAATTC CCCCTATCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1013 CTCCAATTCC CCCTATCATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1014 TCCAATTCCC CCTATCATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1015 CCAATTCCCC CTATCATTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1016 CAATTCCCCC TATCATTTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1017 AATTCCCCCT ATCATTTTTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1018 ATTCCCCCTA TCATTTTTGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1019 TTCCCCCTAT CATTTTTGGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1020 TCCCCCTATC ATTTTTGGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1021 CCCCCTATCA TTTTTGGTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1022 CCCCTATCAT TTTTGGTTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1023 CCCTATCATT TTTGGTTTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1024 CCTATCATTT TTGGTTTCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1025 CTATCATTTT TGGTTTCCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1026 TATCATTTTT GGTTTCCATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1027 ATCATTTTTG GTTTCCATCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1028 TCATTTTTGG TTTCCATCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1029 CATTTTTGGT TTCCATCTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1030 ATTTTTGGTT TCCATCTTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1031 TTTTTGGTTT CCATCTTCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1032 TTTTGGTTTC CATCTTCCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1033 TTTGGTTTCC ATCTTCCTGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1034 TTGGTTTCCA TCTTCCTGGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1035 TGGTTTCCAT CTTCCTGGCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1036 GGTTTCCATC TTCCTGGCAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1037 GTTTCCATCT TCCTGGCAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1038 TTTCCATCTT CCTGGCAAAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1039 TTCCATCTTC CTGGCAAACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1040 TCCATCTTCC TGGCAAACTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1041 CCATCTTCCT GGCAAACTCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1042 CATCTTCCTG GCAAACTCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1043 ATCTTCCTGG CAAACTCATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1044 TCTTCCTGGC AAACTCATTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1045 CTTCCTGGCA AACTCATTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1046 TTCCTGGCAA ACTCATTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1047 TCCTGGCAAA CTCATTTCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1048 CCTGGCAAAC TCATTTCTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1049 CTGGCAAACT CATTTCTTCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1050 TGGCAAACTC ATTTCTTCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1051 GGCAAACTCA TTTCTTCTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1052 GCAAACTCAT TTCTTCTAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1053 CAAACTCATT TCTTCTAATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1054 AAACTCATTT CTTCTAATAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1055 AACTCATTTC TTCTAATACT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1056 ACTCATTTCT TCTAATACTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1057 CTCATTTCTT CTAATACTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1058 TCATTTCTTC TAATACTGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1059 CATTTCTTCT AATACTGTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1060 ATTTCTTCTA ATACTGTATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1061 TTTCTTCTAA TACTGTATCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1062 TTCTTCTAAT ACTGTATCAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1063 TCTTCTAATA CTGTATCATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1064 CTTCTAATAC TGTATCATCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1065 TTCTAATACT GTATCATCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1066 TCTAATACTG TATCATCTGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1067 CTAATACTGT ATCATCTGCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1068 TAATACTGTA TCATCTGCTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1069 AATACTGTAT CATCTGCTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1070 ATACTGTATC ATCTGCTCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1071 TACTGTATCA TCTGCTCCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1072 ACTGTATCAT CTGCTCCTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1073 CTGTATCATC TGCTCCTGTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1074 TGTATCATCT GCTCCTGTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1075 GTATCATCTG CTCCTGTATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1076 TATCATCTGC TCCTGTATCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1077 ATCATCTGCT CCTGTATCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1078 TCATCTGCTC CTGTATCTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1079 CATCTGCTCC TGTATCTAAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1080 ATCTGCTCCT GTATCTAATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1081 TCTGCTCCTG TATCTAATAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1082 CTGCTCCTGT ATCTAATAGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1083 TGCTCCTGTA TCTAATAGAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1084 GCTCCTGTAT CTAATAGAGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1085 CTCCTGTATC TAATAGAGCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1086 TCCTGTATCT AATAGAGCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1087 CCTGTATCTA ATAGAGCTTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1088 CTGTATCTAA TAGAGCTTCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1089 TGTATCTAAT AGAGCTTCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1090 GTATCTAATA GAGCTTCCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1091 TATCTAATAG AGCTTCCTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1092 ATCTAATAGA GCTTCCTTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1093 TCTAATAGAG CTTCCTTTAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1094 CTAATAGAGC TTCCTTTAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1095 TAATAGAGCT TCCTTTAGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1096 AATAGAGCTT CCTTTAGTTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1097 ATAGAGCTTC CTTTAGTTGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1098 TAGAGCTTCC TTTAGTTGCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1099 AGAGCTTCCT TTAGTTGCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1100 GAGCTTCCTT TAGTTGCCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1101 AGCTTCCTTT AGTTGCCCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1102 GCTTCCTTTA GTTGCCCCCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1103 CTTCCTTTAG TTGCCCCCCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1104 TTCCTTTAGT TGCCCCCCTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1105 TCCTTTAGTT GCCCCCCTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1106 CCTTTAGTTG CCCCCCTATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1107 CTTTAGTTGC CCCCCTATCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1108 TTTAGTTGCC CCCCTATCTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1109 TTAGTTGCCC CCCTATCTTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1110 TAGTTGCCCC CCTATCTTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1111 AGTTGCCCCC CTATCTTTAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1112 GTTGCCCCCC TATCTTTATT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1113 TTGCCCCCCT ATCTTTATTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1114 TGCCCCCCTA TCTTTATTGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1115 GCCCCCCTAT CTTTATTGTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1116 CCCCCCTATC TTTATTGTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1117 CCCCCTATCT TTATTGTGAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1118 CCCCTATCTT TATTGTGACG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1119 CCCTATCTTT ATTGTGACGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1120 CCTATCTTTA TTGTGACGAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1121 CTATCTTTAT TGTGACGAGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1122 TATCTTTATT GTGACGAGGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1123 ATCTTTATTG TGACGAGGGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1124 TCTTTATTGT GACGAGGGGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1125 CTTTATTGTG ACGAGGGGTC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1126 TTTATTGTGA CGAGGGGTCG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1127 TTATTGTGAC GAGGGGTCGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1128 TATTGTGACG AGGGGTCGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1129 ATTGTGACGA GGGGTCGTTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1130 TTGTGACGAG GGGTCGTTGC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1131 TGTGACGAGG GGTCGTTGCC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1132 GTGACGAGGG GTCGTTGCCA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1133 TGACGAGGGG TCGTTGCCAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1134 GACGAGGGGT CGTTGCCAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1135 ACGAGGGGTC GTTGCCAAAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1136 CGAGGGGTCG TTGCCAAAGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1137 GAGGGGTCGT TGCCAAAGAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1138 AGGGGTCGTT GCCAAAGAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1139 GGGGTCGTTG CCAAAGAGTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1140 GGGTCGTTGC CAAAGAGTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1141 GGTCGTTGCC AAAGAGTGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1142 GTCGTTGCCA AAGAGTGATC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1143 TCGTTGCCAA AGAGTGATCT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1144 CGTTGCCAAA GAGTGATCTG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1145 GTTGCCAAAG AGTGATCTGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1146 TTGCCAAAGA GTGATCTGAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1147 TGCCAAAGAG TGATCTGAGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1148 GCCAAAGAGT GATCTGAGGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1149 CCAAAGAGTG ATCTGAGGGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1150 CAAAGAGTGA TCTGAGGGAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1151 AAAGAGTGAT CTGAGGGAAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1152 AAGAGTGATC TGAGGGAAGT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1153 AGAGTGATCT GAGGGAAGTT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1154 GAGTGATCTG AGGGAAGTTA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1155 AGTGATCTGA GGGAAGTTAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1156 GTGATCTGAG GGAAGTTAAA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1157 TGATCTGAGG GAAGTTAAAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1158 GATCTGAGGG AAGTTAAAGG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1159 ATCTGAGGGA AGTTAAAGGA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1160 TCTGAGGGAA GTTAAAGGAT 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1161 CTGAGGGAAG TTAAAGGATA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1162 TGAGGGAAGT TAAAGGATAC 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1163 GAGGGAAGTT AAAGGATACA 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1164 AGGGAAGTTA AAGGATACAG 20 20 base pairs nucleic acid single linear cDNA NO NO not provided 1165 GGGAAGTTAA AGGATACAGT 20 

What is claimed is:
 1. A method for predicting the potential of an oligonucleotide to hybridze to a target nucleotide sequence, said method comprising: (a) identifying a predetermined number of unique oligonucleotides of at least 5 nucleotides in length within a nucleotide sequence of at least 30 nucleotides in length that is hybridizable with said target nucleotide sequence, said oligonucleotides being chosen to sample the entire length of said nucleotide sequence, (b) determining and evaluating for each of said oligonucleotides at least one parameter that is independently predictive of the ability of each of said oligonucleotides to hybridize to said target nucleotide sequence, (c) selecting a subset of oligonucleotides within said predetermined number of unique oligonucleotides based on an examination of said parameter and application of a rule that rejects some of said oligonucleotides of step (b), (d) identifying oligonucleotides in said selected subset, viewed according to order of position along said nucleotide sequence, that are clustered along a region of said nucleotide sequence, and, (e) selecting, from said oliaonucleotides identified in step (d), oligonucleotides of higher hybridization potential for said target nucleotide sequence wherein the larger the size of said clusters, the higher said hybridization potential.
 2. A method according to claim 1 which comprises ranking said oligonucleotides of step (e) based on the size of said clusters of oligonucleotides.
 3. A method according to claim 1 wherein said unique oligonucleotides are of identical length N.
 4. A method according to claim 3 wherein said unique oligonucleotides are spaced one nucleotide apart, said predetermined number comprising L−N+1 oligonucleotides, where L is the length of the hybridizable sequence.
 5. A method according to claim 1 wherein said parameter is selected from the group consisting of composition factors, thermodynamic factors, chemosynthetic efficiencies and kinetic factors.
 6. A method according to claim 1 wherein said parameter is a composition factor selected from the group consisting of mole fraction (G+C) and percent (G+C).
 7. A method according to claim 1 wherein said parameter is a thermodynamic factor selected from the group consisting of predicted duplex melting temperature, predicted enthalpy of duplex formation, predicted entropy of duplex formation, predicted free energy of duplex formation, predicted melting temperature of the most stable intramolecular structure of the oligonucleotide or its complement, predicted enthalpy of the most stable intramolecular structure of the oligonucleotide or its complement, predicted entropy of the most stable intramolecular structure of the oligonucleotide or its complement, predicted free energy of the most stable intramolecular structure of the oligonucleotide or its complement, predicted melting temperature of the most stable hairpin structure of the oligonucleotide or its complement, predicted enthalpy of the most stable hairpin structure of the oligonucleotide or its complement, predicted entropy of the most stable hairpin structure of the oligonucleotide or its complement, predicted free energy of the most stable hairpin structure of the oligonucleotide or its complement, thermodynamic partition function for intramolecular structure of the oligonucleotide or its complement.
 8. A method according to claim 1 wherein said parameter is a chemosynthetic efficiency selected from the group consisting of coupling efficiencies and efficiency of the synthesis of a target nucleotide sequence or an oligonucleotide probe.
 9. A method according to claim 1 wherein said parameter is a kinetic factor selected from the group consisting of steric factors calculated via molecular modeling, rate constants calculated via molecular dynamics simulations, rate constants calculated via semi-empirical kinetic modeling, associative rate constants, dissociative rate constants, enthalpies of activation, entropies of activation, and free energies of activation.
 10. A method according to claim 1 wherein said parameter is derived from a factor by mathematical transformation of said factor.
 11. A method according to claim 1 which comprises ranking said clustered oligonucleotides of step (e) based on the size of said clusters of oligonucleotides and selecting a subset of said clustered oligonucleotides.
 12. A method according to claim 11 wherein said subset consists of any number of oligonucleotides within said cluster of oligonucleotides.
 13. A method according to claim 11 wherein the subset of said clustered oligonucleotides are selected to statistically sample the cluster.
 14. A method according to claim 13 wherein said statistical sample consists of oligonucleotides spaced at the first quartile, median and third quartile of the cluster of oligonucleotides.
 15. A method according to claim 1 wherein said parameters are determined for said oligonucleotides by means of a computer program.
 16. A method according to claim 1 wherein said oligonucleotides are attached to a surface.
 17. A method according to claim 1 wherein said oligonucleotides are DNA.
 18. A method according to claim 1 wherein said oligonucleotides are RNA.
 19. A method according to claim 1 wherein said oligonucleotides contain chemically modified nucleotides.
 20. A method according to claim 1 wherein said target nucleotide sequence is RNA.
 21. A method according to claim 1 wherein said target nucleotide sequence is DNA.
 22. A method according to claim 1 wherein said target nucleotide sequence contains chemically modified nucleotides.
 23. A method according to claim 1 wherein said parameter is, for each oligonucleotide/target nucleotide sequence duplex, the difference between the predicted duplex melting temperature corrected for salt concentration and the temperature of hybridization of each of said oligonucleotides with said target nucleotide sequence.
 24. A method according to claim 1 wherein step (c) comprises identifying a subset of oligonucleotides within said predetermined number of unique oligonucleotides by establishing cut-off values for said parameter.
 25. A method according to claim 1 wherein said step (c) comprises identifying a subset of oligonucleotides within said predetermined number of unique oligonucleotides by converting the values of said parameters into a dimensionless number wherein the following equations are used for converting the values of said parameters into a dimensionless number: ${s_{i,x} = \frac{x_{i} - {\langle x\rangle}}{\sigma_{\{ x\}}}},$

where S_(i,x) is the dimensionless score derived from parameter x calculated for oligonucleotide i, x_(i) is the value of parameter x calculated for oligonucleotide i, <x> is the average of parameter x calculated for all of the oligonucleotides under consideration for a given nucleotide sequence target, and σ_({x})is the standard deviation of parameter x calculated for all of the oligonucleotides under consideration for a given nucleotide sequence target, and is given by the equation ${\sigma_{\{ x\}} = \sqrt{\frac{\sum\limits_{j = 1}^{L - N + 1}\left( {x_{j} - {\langle x\rangle}} \right)^{2}}{L - N}}},$

where the target sequence is of length L and the oligonucleotides are of length N.
 26. A method according to claim 25 wherein said value is converted into a dimensionless number by determining a dimensionless score for each parameter resulting in a distribution of scores having a mean value of zero and a standard deviation of one.
 27. A method according to claim 26 which comprises optimizing a method according to calculation for said parameter based on said individual scores.
 28. A method according to claim 1 wherein step (b) comprises determining at least two parameters wherein said parameters are poorly correlated with respect to one another.
 29. A method according to claim 28 wherein said parameters are derived from a combination of factors by mathematical transformation of those factors.
 30. A method according to claim 1 wherein step (b) comprises determining two parameters at least one of said parameters being the association free energy between a subsequence within each of said oligonucleotides and its complementary sequence on said target nucleotide sequence.
 31. A method according to claim 30 wherein said subsequence is 3 to 9 nucleotides in length.
 32. A method according to claim 30 wherein said subsequence is 5 to 7 nucleotides in length.
 33. A method according to claim 30 wherein said subsequence is at least three nucleotides from the terminus of said oligonucleotides.
 34. A method according to claim 30 wherein said subsequence is at least three nucleotides from a surface to which said oligonucleotides are attached.
 35. A method according to claim 30 wherein said oligonucleotides are attached to a surface and said subsequence is at least five nucleotides from the terminus of said oligonucleotides that is attached to said surface and at least three nucleotides from the free end of said oligonucleotides.
 36. A method according to claim 30 wherein the association free energy of the members of a set of subsequences within each of said oligonucleotides is determined and said subsequence having the minimum value is identified.
 37. A method according to claim 1 which comprises including oligonucleotides that are adjacent to said oligonucleotides in said subset that are clustered along a region of said target nucleotide sequence.
 38. A method according to claim 1 which comprises (i) identifying a subset of oligonucleotides within said predetermined number of unique oligonucleotides establishing by cut-off values for each of said parameters.
 39. A method according to claim 1 which comprises determining the sizes of said clusters of step (d) by counting the number of contiguous oligonucleotides in said region of said hybridizable sequence.
 40. A method according to claim 1 which comprises determining the sizes of said clusters of step (d) by counting the number of oligonucleotides in said subset that begin in a region of predetermined length in said hybridizable sequence.
 41. A method for predicting the potential of an oligonucleotide to hybridize to a complementary target nucleotide sequence, said method comprising: (a) identifying a set of overlapping oligonucleotides of at least 5 nucleotides in length from a nucleotide sequence of at least 30 nucleotides in length that is complementary to said target nucleotide sequence, (b) determining and evaluating for each of said oligonucleotides at least two parameters that are independently predictive of the ability of each of said oligonucleotides to hybridize to said target nucleotide sequence wherein said parameters are poorly correlated with respect to one another, (c) selecting a subset of oligonucleotides within said set of oligonucleotides based on an examination of said parameters and application of a rule that rejects some of said oligonucleotides of step (b), (d) identifying oligonucleotides in said selected subset, viewed according to order of position along said nucleotide sequence, that are clustered along a region of said complementary nucleotide sequence, and (e) selecting, from said oligonucleotides identified in step (d), oligonucleotides of higher hybridization potential for said target nucleotide sequence wherein the larger the size of said clusters, the higher said hybridization potential.
 42. A method according to claim 41 which comprises ranking said oligonucleotides of step (e) based on the size of said clusters of oligonucleotides.
 43. A method according to claim 41 which comprises determining the sizes of said clusters of step (e) by counting the number of contiguous oligonucleotides in said region of said complementary sequence.
 44. A method according to claim 41 which comprises determining the sizes of said clusters of step (e) by counting the number of oligonucleotides in said subset that begin in a region of set length in said complementary sequence.
 45. A method according to claim 41 wherein said overlapping oligonucleotides are of identical length N.
 46. A method according to claim 45 wherein said overlapping oligonucleotides are spaced one nucleotide apart, said set comprising L−N+1 oligonucleotides, where L is the length of the complementary sequence.
 47. A method according to claim 41 wherein said parameters are each independently selected from the group consisting of composition factors, thermodynamic factors, chemosynthetic efficiencies and kinetic factors.
 48. A method according to claim 41 wherein said parameters are composition factors selected from the group consisting of mole fraction (G+C) and percent (G+C).
 49. A method according to claim 41 wherein said parameters are thermodynamic factors selected from the group consisting of predicted duplex melting temperature, predicted enthalpy of duplex formation, predicted entropy of duplex formation, predicted free energy of duplex formation, predicted melting temperature of the most stable intramolecular structure of the oligonucleotide or its complement, predicted enthalpy of the most stable intramolecular structure of the oligonucleotide or its complement, predicted entropy of the most stable intramolecular structure of the oligonucleotide or its complement, predicted free energy of the most stable intramolecular structure of the oligonucleotide or its complement, predicted melting temperature of the most stable hairpin structure of the oligonucleotide or its complement, predicted enthalpy of the most stable hairpin structure of the oligonucleotide or its complement, predicted entropy of the most stable hairpin structure of the oligonucleotide or its complement, predicted free energy of the most stable hairpin structure of the oligonucleotide or its complement, thermodynamic partition function for intramolecular structure of the oligonucleotide or its complement.
 50. A method according to claim 41 wherein any of said parameters is derived from a factor by mathematical transformation of said factor.
 51. A method according to claim 49 wherein any of said parameters is derived from a combination of factors by mathematical transformation of those factors.
 52. A method according to claim 41 wherein said parameters are chemosynthetic efficiencies selected from the group consisting of coupling efficiencies and efficiencies of the syntheses of a target nucleotide sequence or an oligonucleotide probe.
 53. method according to claim 41 wherein said parameters are kinetic factors selected from the group consisting of steric factors calculated via molecular modeling, rate constants calculated via molecular dynamics simulations, rate constants calculated via semi-empirical kinetic modeling, associative rate constants, dissociative rate constants, enthalpies of activation, entropies of activation, and free energies of activation.
 54. A method according to claim 41 which comprises ranking said clustered oligonucleotides of step (e) based on the size of said clusters of oligonucleotides and selecting a subset of said clustered oligonucleotides.
 55. A method according to claim 54 wherein said subset consists of any number of oligonucleotides within said cluster of oligonucleotides.
 56. A method according to claim 54 wherein the subset of said clustered oligonucleotides are selected to statistically sample the cluster.
 57. A method according to claim 54 wherein said statistical sample consists of oligonucleotides spaced at the first quartile, median and third quartile of the cluster of oligonucleotides.
 58. A method according to claim 41 wherein said parameters are determined for said oligonucleotides by means of a computer program.
 59. A method according to claim 41 wherein said oligonucleotides are attached to a surface.
 60. A method according to claim 41 wherein said oligonucleotides are DNA.
 61. A method according to claim 41 wherein said oligonucleotides are RNA.
 62. A method according to claim 41 wherein said oligonucleotides contain chemically modified nucleotides.
 63. A method according to claim 41 wherein said target nucleotide sequence is RNA.
 64. A method according to claim 41 wherein said target nucleotide sequence is DNA.
 65. A method according to claim 41 wherein said target nucleotide sequence contains chemically modified nucleotides.
 66. A method according to claim 41 wherein said parameter is, for each oligonucloetide/target nucleotide sequence duplex, the difference between the predicted duplex melting temperature corrected for salt concentration and the temperature of hybridization of each of said oligonucleotides with said target nucleotide sequence.
 67. method according to claim 41 wherein step (c) comprises identifying a subset of oligonucleotides within said set of oligonucleotides by establishing cut-off values for each set of parameters.
 68. A method according to claim 41 wherein said step (c) comprises identifying a subset of oligonucleotides within said set of oligonucleotides by converting the values of said parameters into a dimensionless number wherein the following equations are used for converting the values of said parameters into a dimensionless number: ${s_{i,x} = \frac{x_{i} - {\langle x\rangle}}{\sigma_{\{ x\}}}},$

where S_(i,x) is the dimensionless score derived from parameter x calculated for oligonucleotide i, x_(i) is the value of parameter x calculated for oligonucleotide i, <x> is the average of parameter x calculated for all of the oligonucleotides under consideration for a given nucleotide sequence target, and σ_({x})is the standard deviation of parameter x calculated for all of the oligonucleotides under consideration for a given nucleotide sequence target, and is given by the equation ${\sigma_{\{ x\}} = \sqrt{\frac{\sum\limits_{j = 1}^{L - N + 1}\left( {x_{j} - {\langle x\rangle}} \right)^{2}}{L - N}}},$

where the target sequence is of length L and the oligonucleotides are of length N.
 69. A method according to claim 66 wherein said values are converted into dimensionless numbers by (a) determining a dimensionless score for each parameter resulting in a distribution of scores having a mean value of zero and a standard deviation of one and (b) calculating a combination score by evaluating a weighted average of the individual scores.
 70. A method according to claim 69 wherein step (b) comprises optimizing the weighting factors based on comparison of said individual scores to a calibration data set.
 71. A method according to claim 41 wherein step (b) comprises determining two parameters at least one of said parameters being the association free energy between a subsequence within each of said oligonucleotides and its complementary sequence on said target nucleotide sequence.
 72. A method according to claim 71 wherein said subsequence is 3 to 9 nucleotides in length.
 73. A method according to claim 71 wherein said subsequence is 5 to 7 nucleotides in length.
 74. A method according to claim 71 wherein said subsequence is at least three nucleotides from the terminus of said oligonucleotides.
 75. A method according to claim 71 wherein said oligonucleotides are attached to a surface and said subsequence is at least five nucleotides from the terminus of said oligonucleotides that is attached to said surface and at least three nucleotides from the free end of said oligonucleotides.
 76. A method according to claim 71 wherein the association free energy of the members of a set of subsequences within each of said oligonucleotides is determined and said subsequence having the minimum value is identified.
 77. A method according to claim 41 which comprises including in said evaluation oligonucleotides that are adjacent to said oligonucleotides in said subset that are clustered along a region of said target nucleotide sequence.
 78. A method for predicting the potential of an oligonucleotide to hybridize to a complementary target nucleotide sequence, said method comprising: (a) obtaining, from a nucleotide sequence of at least 30 nucleotides in length complementary to said target nucleotide sequence, a set of overlapping oligonucleotides of at least 5 nucleotides in length and of identical length N and spaced one nucleotide apart, said set comprising L−N+1 oligonucleotides, (b) determining and evaluating for each of said oligonucleotides the parameters: (i) the predicted melt temperature of the duplex of said oligonucleotide and said target nucleotide sequence corrected for salt concentration and (ii) predicted free energy of the most stable intramolecular structure of the oligonucleotide at the temperature of hybridization of each of said oligonucleotides with said target nucleotide sequence, (c) identifying a subset of oligonucleotides within said set of oligonucleotides based on an examination of said parameters by establishing cut-off values for each of said parameters, (d) ranking oligonucleotides in said subset of step (c), viewed according to order of position along said nucleotide sequence, that are clustered along a region of said complementary nucleotide sequence based on the size of said clusters of oligonucleotides, and (e) selecting, based on said ranking, a subset of said clustered oligonucleotides identified in step (d) having higher hybridization potential for said target nucleotide sequence wherein the larger the size of said clusters, the higher said hybridization potential.
 79. A method according to claim 78 wherein said subset consists of any number of oligonucleotides within said cluster of oligonucleotides.
 80. A method according to claim 78 wherein the subset of said clustered oligonucleotides are selected to statistically sample the cluster.
 81. A method according to claim 78 wherein said parameters are derived from a factor by mathematical transformation of said factor.
 82. A method according to claim 78 wherein the melting temperature of step (b) is transform by subtracting the temperature of hybridization.
 83. A method according to claim 78 which comprises determining the sizes of said clusters of step (d) by counting the number of contiguous oligonucleotides in said region of said complementary sequence.
 84. A method according to claim 78 wherein said statistical sample consists of oligonucleotides spaced at the first quartile, median and third quartile of the cluster of oligonucleotides.
 85. A method according to claim 78 wherein said parameters are determined for said oligonucleotides by means of a computer program.
 86. A method according to claim 78 wherein said oligonucleotides are attached to a surface.
 87. A method according to claim 78 wherein said oligonucleotides are DNA.
 88. A method according to claim 78 wherein said oligonucleotides are RNA.
 89. A method according to claim 78 wherein said oligonucleotides contain chemically modified nucleotides.
 90. A method according to claim 78 wherein said target nucleotide sequence is RNA.
 91. A method according to claim 78 wherein said target nucleotide sequence is DNA.
 92. A method according to claim 78 wherein said target nucleotide sequence contains chemically modified nucleotides.
 93. A method according to claim 68 wherein a combination score S_(i) is calculated by evaluating a weighted average of the individual values of the dimensionless scores S_(i,x) by the equation: ${S_{i} = {\sum\limits_{\{ x\}}{q_{x}s_{i,x}}}},$

where q_(x) is the weight assigned to the score derived from parameter x, the individual values of q_(x) are always greater than zero, and the sum of the weights q_(x) is unity.
 94. A method according to claim 78 where clustering is determined by calculating a moving window-averaged combination score <S_(i)> for the ith probe by the equation: ${{\langle S_{i}\rangle} = {\frac{1}{w}{\sum\limits_{j = {i - \frac{w - 1}{2}}}^{i + \frac{w - 1}{2}}S_{j}}}},\quad {w = {{an}\quad {odd}\quad {integer}}},$

where w is the length of the window for averaging, and then applying a cutoff filter to the value of <S_(i)>.
 95. A method according to claim 93 wherein optimization of the weights q_(x) is performed by varying the values of the weights so that the correlation coefficient ρ_({<Si>}, {Vi})between the set of window-averaged combination scores {<S_(i)>} and a set of calibration experimental measurements {V_(i)} is maximized wherein the correlation coefficient ρ_({<Si>},{Vi})is calculated from the equation ${\rho_{x,y} = \frac{{Covariance}\quad \left( {x,y} \right)}{\sqrt{{Variance}\quad (x){Variance}\quad (y)}}},$

where x=<S_(i)>, y=V_(i) and the Covariance (x,y) is defined by ${{Covariance}\quad \left( {x,y} \right)} = {\frac{1}{N}{\sum\limits_{i = 1}^{N}{\left( {x_{i} - \mu_{x}} \right)\left( {y_{i} - \mu_{y}} \right)}}}$

wherein the quantities μ_(x) and μ_(y) are the averages of the quantities x and y, while the variances are the squares of the standard deviations.
 96. A method according to claim 95 wherein the cutoff filter selects the lowest values of the window-averaged combination score <S_(i)> and the clustered probes so identified are predicted to exhibit low hybridization efficiency.
 97. A computer based method for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence, said method comprising: (a) identifying under computer control a predetermined number of unique oligonucleotides of at least 5 nucleotides in length within a nucleotide sequence of at least 30 nucleotides in length that is hybridizable with said target nucleotide sequence, said oligonucleotides being chosen to sample the entire length of said nucleotide sequence, (b) under computer control, determining and evaluating for each of said oligonucleotides a value for at least one parameter that is independently predictive of the ability of each of said oligonucleotides to hybridize to said target nucleotide sequence and storing said parameter values, (c) selecting under computer control, from said stored parameter values, a subset of oligonucleotides within said predetermined number of unique oligonucleotides based on an examination of said parameter and application of a rule that rejects some of said oligonucleotides of step (b), (d) identifying under computer control oligonucleotides in said selected subset, viewed according to order of position along said nucleotide sequence, that are clustered along a region of said nucleotide sequence that is hybridizable to said target nucleotide sequence, and (e) under computer control selecting, from said oligonucleotides identified in step (d), oligonucleotides of higher hybridization potential for said target nucleotide sequence wherein the larger the size of said clusters, the higher said hybridization potential.
 98. A method according to claim 97 wherein the identified subset of oligonucleotide sequences is electronically transferred to an oligonucleotide array manufacturing system. 